brainImaging/notebooks/freesurferAnalysisNative.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Freesurfer fMRI preprocessing, design setup and result estimation"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### set directory names"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "projectDir=\"/data/martin/prosopagnosia/\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "nbDir=${projectDir}\"notebooks/\"\n",
    "dicomDir=${projectDir}\"DCM/\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### get DICOMs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "cd $dicomDir"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[0m\u001b[34;42m09190000\u001b[0m  \u001b[34;42m09190001\u001b[0m  \u001b[34;42m09190002\u001b[0m\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Commands used for dcmunpack:  \n",
    "\n",
    "- src: says where the files are\n",
    "- index-out: saves a list of all the files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "cd /data/martin/prosopagnosia/DCM\n",
      "/usr/local/freesurfer/bin/dcmunpack -src . -index-out dcm.index.dat\n",
      "\n",
      "-rwxrwxr-x 1 8481 1590 23759 Jan 18  2017 /usr/local/freesurfer/bin/dcmunpack\n",
      "---------------------------------------\n",
      "---------------------------------------\n",
      "Searching for matching files\n",
      "Fri Nov 24 12:54:34 CET 2017\n",
      "Fri Nov 24 12:54:34 CET 2017\n",
      "Found 2683 total files.\n",
      "  Interrogating each and every one of them.\n",
      "  Be patient.\n",
      "If you have collected the data in the Martinos center, this \n",
      "will run faster if you kill this job and re-run with -martinos \n",
      "Except, with changes in the file naming (Oct 2012), this does \n",
      "not work.\n",
      "Found 34 unique series: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34\n",
      "Subject ANONYMIZED\n",
      "Date 19890323\n",
      "Time 150358.109000\n",
      "Institution EVKB Mara 1\n",
      "cat: write error: Broken pipe\n",
      "1 localizer 4 8.6 20 0.48828125 COL 320 ./09190000/84756842.dcm\n",
      "cat: write error: Broken pipe\n",
      "2 t1_fl2d_sag_p2 2.49 280 70 0.44921875 ROW 268 ./09190000/84756884.dcm\n",
      "cat: write error: Broken pipe\n",
      "3 ep2d_pace_moco_localizer 30 3000 80 unknown COL 1563 ./09190000/84755191.dcm\n",
      "cat: write error: Broken pipe\n",
      "4 MoCoSeries 30 3000 80 unknown COL 1563 ./09190000/84752078.dcm\n",
      "cat: write error: Broken pipe\n",
      "5 ep2d_pace_moco_localizer 30 3000 80 unknown COL 1563 ./09190000/84748613.dcm\n",
      "cat: write error: Broken pipe\n",
      "6 MoCoSeries 30 3000 80 unknown COL 1563 ./09190000/84747058.dcm\n",
      "cat: write error: Broken pipe\n",
      "7 localizer 4 8.6 20 0.48828125 COL 320 ./09190000/84746310.dcm\n",
      "cat: write error: Broken pipe\n",
      "8 t1_fl2d_sag_p2 2.49 280 70 0.44921875 ROW 268 ./09190000/84746384.dcm\n",
      "cat: write error: Broken pipe\n",
      "9 t1_fl2d_cor_p2 2.49 280 70 0.44921875 ROW 268 ./09190000/84743700.dcm\n",
      "cat: write error: Broken pipe\n",
      "10 t1_fl2d_tra_p2 2.46 220 70 0.4296875 ROW 320 ./09190000/84743988.dcm\n",
      "cat: write error: Broken pipe\n",
      "11 Mag_Images 20 27 15 0.8984375 ROW 120 ./09190000/84744276.dcm\n",
      "cat: write error: Broken pipe\n",
      "12 Pha_Images 20 27 15 0.8984375 ROW 120 ./09190000/84741868.dcm\n",
      "cat: write error: Broken pipe\n",
      "13 mIP_ImagesSW 20 27 15 0.8984375 ROW 120 ./09190000/84740188.dcm\n",
      "cat: write error: Broken pipe\n",
      "14 SWI_Images 20 27 15 0.8984375 ROW 120 ./09190000/84740956.dcm\n",
      "cat: write error: Broken pipe\n",
      "15 flair_tra_4mm_0,7x0,7_fs 128 8000 160 0.66666668653488 ROW 200 ./09190001/84737475.dcm\n",
      "cat: write error: Broken pipe\n",
      "16 gre_field_mapping 5.19 400 60 3.125\\3.125 COL 260 ./09190001/84737731.dcm\n",
      "cat: write error: Broken pipe\n",
      "17 gre_field_mapping 7.65 400 60 3.125\\3.125 COL 260 ./09190001/84735784.dcm\n",
      "cat: write error: Broken pipe\n",
      "18 StartFMRI 33 3000 90 2.4000000953674\\2.4000000953674 COL 2232 ./09190001/84736138.dcm\n",
      "cat: write error: Broken pipe\n",
      "19 ep2d_bold_moco_kissler_4mm_hohe_matrix_kurzeTE_pace 33 3000 90 2.4000000953674\\2.4000000953674 COL 2232 ./09190001/84734305.dcm\n",
      "cat: write error: Broken pipe\n",
      "20 bas_MoCoSeries 33 3000 90 2.4000000953674\\2.4000000953674 COL 2232 ./09190001/84730840.dcm\n",
      "cat: write error: Broken pipe\n",
      "21 intermediatet-Map 33 3000 90 2.4000000953674\\2.4000000953674 COL 2232 ./09190001/84729285.dcm\n",
      "cat: write error: Broken pipe\n",
      "22 Design 33 3000 90 0.001 COL 2232 ./09190001/84727700.dcm\n",
      "cat: write error: Broken pipe\n",
      "23 EvaSeries_GLM 33 3000 90 2.4000000953674\\2.4000000953674 COL 2232 ./09190001/84727716.dcm\n",
      "cat: write error: Broken pipe\n",
      "24 Mean_&_t-Maps 33 3000 90 2.4000000953674\\2.4000000953674 COL 2232 ./09190001/84727732.dcm\n",
      "cat: write error: Broken pipe\n",
      "25 t1_mpr_sag_p2_iso0,9_320:- 2.5 1900 9 0.75 ROW 180 ./09190001/84723732.dcm\n",
      "cat: write error: Broken pipe\n",
      "26 gre_field_mapping 7.65 542 60 4.375\\4.375 COL 260 ./09190001/84723893.dcm\n",
      "27 <MPR-ModusSerie> 2.5 1900 9 0.75 ROW 180 ./09190002/84718414.dcm\n",
      "28 <MPR-ModusSerie[1]> 2.5 1900 9 0.75 ROW 180 ./09190002/84714235.dcm\n",
      "cat: write error: Broken pipe\n",
      "29 ep2d_diff_mddw_30_p2 83 15300 90 unknown COL 1698 ./09190001/84714530.dcm\n",
      "cat: write error: Broken pipe\n",
      "30 ep2d_diff_mddw_30_p2_ADC 83 15300 90 unknown COL 1698 ./09190001/84712687.dcm\n",
      "cat: write error: Broken pipe\n",
      "31 ep2d_diff_mddw_30_p2_TRACEW 83 15300 90 unknown COL 1698 ./09190001/84710713.dcm\n",
      "cat: write error: Broken pipe\n",
      "32 ep2d_diff_mddw_30_p2_FA 83 15300 90 unknown COL 1698 ./09190001/84711993.dcm\n",
      "cat: write error: Broken pipe\n",
      "33 ep2d_diff_mddw_30_p2_ColFA unknown unknown unknown unknown unknown unknown ./09190001/84709829.dcm\n",
      "34 ep2d_diff_mddw_30_p2_TENSOR unknown unknown unknown unknown unknown unknown ./09190002/84710384.dcm\n",
      "\n",
      "\n",
      "Fri Nov 24 12:58:22 CET 2017\n",
      "dcmunpack done\n"
     ]
    }
   ],
   "source": [
    "dcmunpack -src . -index-out dcm.index.dat"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "get the relevant fmri sessions into correct folder structure"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "cd /data/martin/prosopagnosia/DCM\n",
      "/usr/local/freesurfer/bin/dcmunpack -src . -index-in dcm.index.dat -targ /data/martin/prosopagnosia/landscapes/Sess01 -run 3 bold nii f.nii\n",
      "\n",
      "-rwxrwxr-x 1 8481 1590 23759 Jan 18  2017 /usr/local/freesurfer/bin/dcmunpack\n",
      "---------------------------------------\n",
      "  1 3 bold f 0 0\n",
      "---------------------------------------\n",
      "Searching for matching files\n",
      "Fri Nov 24 12:58:22 CET 2017\n",
      "Fri Nov 24 12:58:22 CET 2017\n",
      "Found 2684 total files.\n",
      "Found 34 unique series: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34\n",
      "Subject ANONYMIZED\n",
      "Date 19890323\n",
      "Time 150358.109000\n",
      "Institution EVKB Mara 1\n",
      "cat: write error: Broken pipe\n",
      "1 localizer 4 8.6 20 0.48828125 COL 320 ./09190000/84756842.dcm\n",
      "cat: write error: Broken pipe\n",
      "2 t1_fl2d_sag_p2 2.49 280 70 0.44921875 ROW 268 ./09190000/84756884.dcm\n",
      "cat: write error: Broken pipe\n",
      "3 ep2d_pace_moco_localizer 30 3000 80 unknown COL 1563 ./09190000/84755191.dcm\n",
      "cat: write error: Broken pipe\n",
      "4 MoCoSeries 30 3000 80 unknown COL 1563 ./09190000/84752078.dcm\n",
      "cat: write error: Broken pipe\n",
      "5 ep2d_pace_moco_localizer 30 3000 80 unknown COL 1563 ./09190000/84748613.dcm\n",
      "cat: write error: Broken pipe\n",
      "6 MoCoSeries 30 3000 80 unknown COL 1563 ./09190000/84747058.dcm\n",
      "cat: write error: Broken pipe\n",
      "7 localizer 4 8.6 20 0.48828125 COL 320 ./09190000/84746310.dcm\n",
      "cat: write error: Broken pipe\n",
      "8 t1_fl2d_sag_p2 2.49 280 70 0.44921875 ROW 268 ./09190000/84746384.dcm\n",
      "cat: write error: Broken pipe\n",
      "9 t1_fl2d_cor_p2 2.49 280 70 0.44921875 ROW 268 ./09190000/84743700.dcm\n",
      "cat: write error: Broken pipe\n",
      "10 t1_fl2d_tra_p2 2.46 220 70 0.4296875 ROW 320 ./09190000/84743988.dcm\n",
      "cat: write error: Broken pipe\n",
      "11 Mag_Images 20 27 15 0.8984375 ROW 120 ./09190000/84744276.dcm\n",
      "cat: write error: Broken pipe\n",
      "12 Pha_Images 20 27 15 0.8984375 ROW 120 ./09190000/84741868.dcm\n",
      "cat: write error: Broken pipe\n",
      "13 mIP_ImagesSW 20 27 15 0.8984375 ROW 120 ./09190000/84740188.dcm\n",
      "cat: write error: Broken pipe\n",
      "14 SWI_Images 20 27 15 0.8984375 ROW 120 ./09190000/84740956.dcm\n",
      "cat: write error: Broken pipe\n",
      "15 flair_tra_4mm_0,7x0,7_fs 128 8000 160 0.66666668653488 ROW 200 ./09190001/84737475.dcm\n",
      "cat: write error: Broken pipe\n",
      "16 gre_field_mapping 5.19 400 60 3.125\\3.125 COL 260 ./09190001/84737731.dcm\n",
      "cat: write error: Broken pipe\n",
      "17 gre_field_mapping 7.65 400 60 3.125\\3.125 COL 260 ./09190001/84735784.dcm\n",
      "cat: write error: Broken pipe\n",
      "18 StartFMRI 33 3000 90 2.4000000953674\\2.4000000953674 COL 2232 ./09190001/84736138.dcm\n",
      "cat: write error: Broken pipe\n",
      "19 ep2d_bold_moco_kissler_4mm_hohe_matrix_kurzeTE_pace 33 3000 90 2.4000000953674\\2.4000000953674 COL 2232 ./09190001/84734305.dcm\n",
      "cat: write error: Broken pipe\n",
      "20 bas_MoCoSeries 33 3000 90 2.4000000953674\\2.4000000953674 COL 2232 ./09190001/84730840.dcm\n",
      "cat: write error: Broken pipe\n",
      "21 intermediatet-Map 33 3000 90 2.4000000953674\\2.4000000953674 COL 2232 ./09190001/84729285.dcm\n",
      "cat: write error: Broken pipe\n",
      "22 Design 33 3000 90 0.001 COL 2232 ./09190001/84727700.dcm\n",
      "cat: write error: Broken pipe\n",
      "23 EvaSeries_GLM 33 3000 90 2.4000000953674\\2.4000000953674 COL 2232 ./09190001/84727716.dcm\n",
      "cat: write error: Broken pipe\n",
      "24 Mean_&_t-Maps 33 3000 90 2.4000000953674\\2.4000000953674 COL 2232 ./09190001/84727732.dcm\n",
      "cat: write error: Broken pipe\n",
      "25 t1_mpr_sag_p2_iso0,9_320:- 2.5 1900 9 0.75 ROW 180 ./09190001/84723732.dcm\n",
      "cat: write error: Broken pipe\n",
      "26 gre_field_mapping 7.65 542 60 4.375\\4.375 COL 260 ./09190001/84723893.dcm\n",
      "27 <MPR-ModusSerie> 2.5 1900 9 0.75 ROW 180 ./09190002/84718414.dcm\n",
      "28 <MPR-ModusSerie[1]> 2.5 1900 9 0.75 ROW 180 ./09190002/84714235.dcm\n",
      "cat: write error: Broken pipe\n",
      "29 ep2d_diff_mddw_30_p2 83 15300 90 unknown COL 1698 ./09190001/84714530.dcm\n",
      "cat: write error: Broken pipe\n",
      "30 ep2d_diff_mddw_30_p2_ADC 83 15300 90 unknown COL 1698 ./09190001/84712687.dcm\n",
      "cat: write error: Broken pipe\n",
      "31 ep2d_diff_mddw_30_p2_TRACEW 83 15300 90 unknown COL 1698 ./09190001/84710713.dcm\n",
      "cat: write error: Broken pipe\n",
      "32 ep2d_diff_mddw_30_p2_FA 83 15300 90 unknown COL 1698 ./09190001/84711993.dcm\n",
      "cat: write error: Broken pipe\n",
      "33 ep2d_diff_mddw_30_p2_ColFA unknown unknown unknown unknown unknown unknown ./09190001/84709829.dcm\n",
      "34 ep2d_diff_mddw_30_p2_TENSOR unknown unknown unknown unknown unknown unknown ./09190002/84710384.dcm\n",
      "mri_convert.bin ./09190000/84755191.dcm /data/martin/prosopagnosia/landscapes/Sess01/bold/003/f.nii --nskip 0 --ndrop 0 \n",
      "nskip = 0\n",
      "ndrop = 0\n",
      "$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $\n",
      "reading from ./09190000/84755191.dcm...\n",
      "Getting Series No \n",
      "INFO: Found 1002 files in ./09190000\n",
      "INFO: Scanning for Series Number 3\n",
      "Scanning Directory \n",
      "INFO: found 170 files in series\n",
      "INFO: loading series header info.\n",
      "\n",
      "RunNo = 2\n",
      "WARNING: Run 1 appears to be truncated\n",
      "  Files Found: 170, Files Expected (lRep+1): 200\n",
      "FileName \t\t./09190000/84757220.dcm\n",
      "Identification\n",
      "\tNumarisVer        syngo MR B19\n",
      "\tScannerModel      Verio \n",
      "\tPatientName       ANONYMIZED    \n",
      "Date and time\n",
      "\tStudyDate         19890323\n",
      "\tStudyTime         150358.109000 \n",
      "\tSeriesTime        151201.187000 \n",
      "\tAcqTime           151056.187500 \n",
      "Acquisition parameters\n",
      "\tPulseSeq          *epfid2d1_128 \n",
      "\tProtocol          ep2d_pace_moco_localizer\n",
      "\tPhEncDir          COL\n",
      "\tEchoNo            1\n",
      "\tFlipAngle         80\n",
      "\tEchoTime          30\n",
      "\tInversionTime     -1\n",
      "\tRepetitionTime    3000\n",
      "\tPhEncFOV          256\n",
      "\tReadoutFOV        256\n",
      "Image information\n",
      "\tRunNo             2\n",
      "\tSeriesNo          3\n",
      "\tImageNo           1\n",
      "\tNImageRows        896\n",
      "\tNImageCols        896\n",
      "\tNFrames           170\n",
      "\tSliceArraylSize   40\n",
      "\tIsMosaic          1\n",
      "\tImgPos            880.9352 888.1388 138.5043 \n",
      "\tVolRes              2.0000   2.0000   2.0000 \n",
      "\tVolDim            128      128       40 \n",
      "\tVc                 -0.9995  -0.0273   0.0181 \n",
      "\tVr                  0.0227  -0.9755  -0.2188 \n",
      "\tVs                  0.0237  -0.2183   0.9756 \n",
      "\tVolCenter           0.0000   0.0000   0.0000 \n",
      "\tTransferSyntaxUID 1.2.840.10008.1.2.1\n",
      "INFO: sorting.\n",
      "INFO: (128 128  40), nframes = 170, ismosaic=1\n",
      "sdfi->UseSliceScaleFactor 0\n",
      "datatype = 4, short=4, float=3\n",
      "Could not parse NUMARIS version string syngo MR B19\n",
      "found in dicom tag 18,1020 (len = 3 != 6)\n",
      "Repetition Time = 3000, TR = 3000 ms\n",
      "PE Dir COL COL\n",
      "AutoAlign matrix detected \n",
      "AutoAlign Matrix --------------------- \n",
      " 1.00000   0.00000   0.00000   0.00000;\n",
      " 0.00000   1.00000   0.00000   0.00000;\n",
      " 0.00000   0.00000   1.00000   0.00000;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "FileName \t\t./09190000/84757220.dcm\n",
      "Identification\n",
      "\tNumarisVer        syngo MR B19\n",
      "\tScannerModel      Verio \n",
      "\tPatientName       ANONYMIZED    \n",
      "Date and time\n",
      "\tStudyDate         19890323\n",
      "\tStudyTime         150358.109000 \n",
      "\tSeriesTime        151201.187000 \n",
      "\tAcqTime           151056.187500 \n",
      "Acquisition parameters\n",
      "\tPulseSeq          *epfid2d1_128 \n",
      "\tProtocol          ep2d_pace_moco_localizer\n",
      "\tPhEncDir          COL\n",
      "\tEchoNo            1\n",
      "\tFlipAngle         80\n",
      "\tEchoTime          30\n",
      "\tInversionTime     -1\n",
      "\tRepetitionTime    3000\n",
      "\tPhEncFOV          256\n",
      "\tReadoutFOV        256\n",
      "Image information\n",
      "\tRunNo             2\n",
      "\tSeriesNo          3\n",
      "\tImageNo           1\n",
      "\tNImageRows        896\n",
      "\tNImageCols        896\n",
      "\tNFrames           170\n",
      "\tSliceArraylSize   40\n",
      "\tIsMosaic          1\n",
      "\tImgPos            130.7667 117.9778 -15.5974 \n",
      "\tVolRes              2.0000   2.0000   2.0000 \n",
      "\tVolDim            128      128       40 \n",
      "\tVc                 -0.9995  -0.0273   0.0181 \n",
      "\tVr                  0.0227  -0.9755  -0.2188 \n",
      "\tVs                  0.0237  -0.2183   0.9756 \n",
      "\tVolCenter           6.6849 -19.1124  -2.2568 \n",
      "\tTransferSyntaxUID 1.2.840.10008.1.2.1\n",
      "UseSliceScaleFactor 0 (slice 0: 1)\n",
      "IsDWI = 0\n",
      "sagrev = 0, correv =0, trarev = 0\n",
      "Vs = 0.0236561 -0.218251 0.975606\n",
      "INFO: no Siemens slice order reversal detected (good!). \n",
      "TR=3000.00, TE=30.00, TI=-1.00, flip angle=80.00\n",
      "i_ras = (-0.999463, -0.0273032, 0.0181267)\n",
      "j_ras = (0.022681, -0.975511, -0.21878)\n",
      "k_ras = (0.0236561, -0.218251, 0.975606)\n",
      "writing to /data/martin/prosopagnosia/landscapes/Sess01/bold/003/f.nii...\n",
      "Started at Fri Nov 24 12:58:22 CET 2017 \n",
      "Ended   at Fri Nov 24 12:58:42 CET 2017\n",
      "dcmunpack-Run-Time-Min 0.33\n",
      "\n",
      "\n",
      "Fri Nov 24 12:58:42 CET 2017\n",
      "dcmunpack done\n"
     ]
    }
   ],
   "source": [
    "dcmunpack -src . -index-in dcm.index.dat -targ ${projectDir}\"landscapes/Sess01\" -run 3 bold nii f.nii"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[34;42m/data/martin/prosopagnosia/landscapes\u001b[00m\n",
      "└── \u001b[34;42mSess01\u001b[00m\n",
      "    ├── \u001b[34;42mbold\u001b[00m\n",
      "    │   └── \u001b[34;42m003\u001b[00m\n",
      "    │       ├── \u001b[01;32mf-infodump.dat\u001b[00m\n",
      "    │       └── \u001b[01;32mf.nii\u001b[00m\n",
      "    ├── \u001b[01;32mdcmunpack.log\u001b[00m\n",
      "    ├── \u001b[01;32mimagelist.dat\u001b[00m\n",
      "    └── \u001b[01;32mseries-info.dat\u001b[00m\n",
      "\n",
      "3 directories, 5 files\n"
     ]
    }
   ],
   "source": [
    "tree ${projectDir}landscapes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "cd /data/martin/prosopagnosia/DCM\n",
      "/usr/local/freesurfer/bin/dcmunpack -src . -index-in dcm.index.dat -targ /data/martin/prosopagnosia/hands/Sess01 -run 5 bold nii f.nii\n",
      "\n",
      "-rwxrwxr-x 1 8481 1590 23759 Jan 18  2017 /usr/local/freesurfer/bin/dcmunpack\n",
      "---------------------------------------\n",
      "  1 5 bold f 0 0\n",
      "---------------------------------------\n",
      "Searching for matching files\n",
      "Fri Nov 24 12:58:43 CET 2017\n",
      "Fri Nov 24 12:58:43 CET 2017\n",
      "Found 2684 total files.\n",
      "Found 34 unique series: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34\n",
      "Subject ANONYMIZED\n",
      "Date 19890323\n",
      "Time 150358.109000\n",
      "Institution EVKB Mara 1\n",
      "cat: write error: Broken pipe\n",
      "1 localizer 4 8.6 20 0.48828125 COL 320 ./09190000/84756842.dcm\n",
      "cat: write error: Broken pipe\n",
      "2 t1_fl2d_sag_p2 2.49 280 70 0.44921875 ROW 268 ./09190000/84756884.dcm\n",
      "cat: write error: Broken pipe\n",
      "3 ep2d_pace_moco_localizer 30 3000 80 unknown COL 1563 ./09190000/84755191.dcm\n",
      "cat: write error: Broken pipe\n",
      "4 MoCoSeries 30 3000 80 unknown COL 1563 ./09190000/84752078.dcm\n",
      "cat: write error: Broken pipe\n",
      "5 ep2d_pace_moco_localizer 30 3000 80 unknown COL 1563 ./09190000/84748613.dcm\n",
      "cat: write error: Broken pipe\n",
      "6 MoCoSeries 30 3000 80 unknown COL 1563 ./09190000/84747058.dcm\n",
      "cat: write error: Broken pipe\n",
      "7 localizer 4 8.6 20 0.48828125 COL 320 ./09190000/84746310.dcm\n",
      "cat: write error: Broken pipe\n",
      "8 t1_fl2d_sag_p2 2.49 280 70 0.44921875 ROW 268 ./09190000/84746384.dcm\n",
      "cat: write error: Broken pipe\n",
      "9 t1_fl2d_cor_p2 2.49 280 70 0.44921875 ROW 268 ./09190000/84743700.dcm\n",
      "cat: write error: Broken pipe\n",
      "10 t1_fl2d_tra_p2 2.46 220 70 0.4296875 ROW 320 ./09190000/84743988.dcm\n",
      "cat: write error: Broken pipe\n",
      "11 Mag_Images 20 27 15 0.8984375 ROW 120 ./09190000/84744276.dcm\n",
      "cat: write error: Broken pipe\n",
      "12 Pha_Images 20 27 15 0.8984375 ROW 120 ./09190000/84741868.dcm\n",
      "cat: write error: Broken pipe\n",
      "13 mIP_ImagesSW 20 27 15 0.8984375 ROW 120 ./09190000/84740188.dcm\n",
      "cat: write error: Broken pipe\n",
      "14 SWI_Images 20 27 15 0.8984375 ROW 120 ./09190000/84740956.dcm\n",
      "cat: write error: Broken pipe\n",
      "15 flair_tra_4mm_0,7x0,7_fs 128 8000 160 0.66666668653488 ROW 200 ./09190001/84737475.dcm\n",
      "cat: write error: Broken pipe\n",
      "16 gre_field_mapping 5.19 400 60 3.125\\3.125 COL 260 ./09190001/84737731.dcm\n",
      "cat: write error: Broken pipe\n",
      "17 gre_field_mapping 7.65 400 60 3.125\\3.125 COL 260 ./09190001/84735784.dcm\n",
      "cat: write error: Broken pipe\n",
      "18 StartFMRI 33 3000 90 2.4000000953674\\2.4000000953674 COL 2232 ./09190001/84736138.dcm\n",
      "cat: write error: Broken pipe\n",
      "19 ep2d_bold_moco_kissler_4mm_hohe_matrix_kurzeTE_pace 33 3000 90 2.4000000953674\\2.4000000953674 COL 2232 ./09190001/84734305.dcm\n",
      "cat: write error: Broken pipe\n",
      "20 bas_MoCoSeries 33 3000 90 2.4000000953674\\2.4000000953674 COL 2232 ./09190001/84730840.dcm\n",
      "cat: write error: Broken pipe\n",
      "21 intermediatet-Map 33 3000 90 2.4000000953674\\2.4000000953674 COL 2232 ./09190001/84729285.dcm\n",
      "cat: write error: Broken pipe\n",
      "22 Design 33 3000 90 0.001 COL 2232 ./09190001/84727700.dcm\n",
      "cat: write error: Broken pipe\n",
      "23 EvaSeries_GLM 33 3000 90 2.4000000953674\\2.4000000953674 COL 2232 ./09190001/84727716.dcm\n",
      "cat: write error: Broken pipe\n",
      "24 Mean_&_t-Maps 33 3000 90 2.4000000953674\\2.4000000953674 COL 2232 ./09190001/84727732.dcm\n",
      "cat: write error: Broken pipe\n",
      "25 t1_mpr_sag_p2_iso0,9_320:- 2.5 1900 9 0.75 ROW 180 ./09190001/84723732.dcm\n",
      "cat: write error: Broken pipe\n",
      "26 gre_field_mapping 7.65 542 60 4.375\\4.375 COL 260 ./09190001/84723893.dcm\n",
      "27 <MPR-ModusSerie> 2.5 1900 9 0.75 ROW 180 ./09190002/84718414.dcm\n",
      "28 <MPR-ModusSerie[1]> 2.5 1900 9 0.75 ROW 180 ./09190002/84714235.dcm\n",
      "cat: write error: Broken pipe\n",
      "29 ep2d_diff_mddw_30_p2 83 15300 90 unknown COL 1698 ./09190001/84714530.dcm\n",
      "cat: write error: Broken pipe\n",
      "30 ep2d_diff_mddw_30_p2_ADC 83 15300 90 unknown COL 1698 ./09190001/84712687.dcm\n",
      "cat: write error: Broken pipe\n",
      "31 ep2d_diff_mddw_30_p2_TRACEW 83 15300 90 unknown COL 1698 ./09190001/84710713.dcm\n",
      "cat: write error: Broken pipe\n",
      "32 ep2d_diff_mddw_30_p2_FA 83 15300 90 unknown COL 1698 ./09190001/84711993.dcm\n",
      "cat: write error: Broken pipe\n",
      "33 ep2d_diff_mddw_30_p2_ColFA unknown unknown unknown unknown unknown unknown ./09190001/84709829.dcm\n",
      "34 ep2d_diff_mddw_30_p2_TENSOR unknown unknown unknown unknown unknown unknown ./09190002/84710384.dcm\n",
      "mri_convert.bin ./09190000/84748613.dcm /data/martin/prosopagnosia/hands/Sess01/bold/005/f.nii --nskip 0 --ndrop 0 \n",
      "nskip = 0\n",
      "ndrop = 0\n",
      "$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $\n",
      "reading from ./09190000/84748613.dcm...\n",
      "Getting Series No \n",
      "INFO: Found 1002 files in ./09190000\n",
      "INFO: Scanning for Series Number 5\n",
      "Scanning Directory \n",
      "INFO: found 200 files in series\n",
      "INFO: loading series header info.\n",
      "\n",
      "RunNo = 4\n",
      "INFO: sorting.\n",
      "INFO: (128 128  40), nframes = 200, ismosaic=1\n",
      "sdfi->UseSliceScaleFactor 0\n",
      "datatype = 4, short=4, float=3\n",
      "Could not parse NUMARIS version string syngo MR B19\n",
      "found in dicom tag 18,1020 (len = 3 != 6)\n",
      "Repetition Time = 3000, TR = 3000 ms\n",
      "PE Dir COL COL\n",
      "AutoAlign matrix detected \n",
      "AutoAlign Matrix --------------------- \n",
      " 1.00000   0.00000   0.00000   0.00000;\n",
      " 0.00000   1.00000   0.00000   0.00000;\n",
      " 0.00000   0.00000   1.00000   0.00000;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "FileName \t\t./09190000/84752926.dcm\n",
      "Identification\n",
      "\tNumarisVer        syngo MR B19\n",
      "\tScannerModel      Verio \n",
      "\tPatientName       ANONYMIZED    \n",
      "Date and time\n",
      "\tStudyDate         19890323\n",
      "\tStudyTime         150358.109000 \n",
      "\tSeriesTime        152210.468000 \n",
      "\tAcqTime           152105.027500 \n",
      "Acquisition parameters\n",
      "\tPulseSeq          *epfid2d1_128 \n",
      "\tProtocol          ep2d_pace_moco_localizer\n",
      "\tPhEncDir          COL\n",
      "\tEchoNo            1\n",
      "\tFlipAngle         80\n",
      "\tEchoTime          30\n",
      "\tInversionTime     -1\n",
      "\tRepetitionTime    3000\n",
      "\tPhEncFOV          256\n",
      "\tReadoutFOV        256\n",
      "Image information\n",
      "\tRunNo             4\n",
      "\tSeriesNo          5\n",
      "\tImageNo           1\n",
      "\tNImageRows        896\n",
      "\tNImageCols        896\n",
      "\tNFrames           200\n",
      "\tSliceArraylSize   40\n",
      "\tIsMosaic          1\n",
      "\tImgPos            130.7667 117.9778 -15.5974 \n",
      "\tVolRes              2.0000   2.0000   2.0000 \n",
      "\tVolDim            128      128       40 \n",
      "\tVc                 -0.9995  -0.0273   0.0181 \n",
      "\tVr                  0.0227  -0.9755  -0.2188 \n",
      "\tVs                  0.0237  -0.2183   0.9756 \n",
      "\tVolCenter           6.6849 -19.1124  -2.2568 \n",
      "\tTransferSyntaxUID 1.2.840.10008.1.2.1\n",
      "UseSliceScaleFactor 0 (slice 0: 1)\n",
      "IsDWI = 0\n",
      "sagrev = 0, correv =0, trarev = 0\n",
      "Vs = 0.0236561 -0.218251 0.975606\n",
      "INFO: no Siemens slice order reversal detected (good!). \n",
      "TR=3000.00, TE=30.00, TI=-1.00, flip angle=80.00\n",
      "i_ras = (-0.999463, -0.0273032, 0.0181267)\n",
      "j_ras = (0.022681, -0.975511, -0.21878)\n",
      "k_ras = (0.0236561, -0.218251, 0.975606)\n",
      "writing to /data/martin/prosopagnosia/hands/Sess01/bold/005/f.nii...\n",
      "Started at Fri Nov 24 12:58:43 CET 2017 \n",
      "Ended   at Fri Nov 24 12:59:05 CET 2017\n",
      "dcmunpack-Run-Time-Min 0.37\n",
      "\n",
      "\n",
      "Fri Nov 24 12:59:05 CET 2017\n",
      "dcmunpack done\n"
     ]
    }
   ],
   "source": [
    "dcmunpack -src . -index-in dcm.index.dat -targ ${projectDir}\"hands/Sess01\" -run 5 bold nii f.nii"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[34;42m/data/martin/prosopagnosia/hands\u001b[00m\n",
      "└── \u001b[34;42mSess01\u001b[00m\n",
      "    ├── \u001b[34;42mbold\u001b[00m\n",
      "    │   └── \u001b[34;42m005\u001b[00m\n",
      "    │       ├── \u001b[01;32mf-infodump.dat\u001b[00m\n",
      "    │       └── \u001b[01;32mf.nii\u001b[00m\n",
      "    ├── \u001b[01;32mdcmunpack.log\u001b[00m\n",
      "    ├── \u001b[01;32mimagelist.dat\u001b[00m\n",
      "    └── \u001b[01;32mseries-info.dat\u001b[00m\n",
      "\n",
      "3 directories, 5 files\n"
     ]
    }
   ],
   "source": [
    "tree ${projectDir}hands"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### get rid of dummy scans"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "mri_convert.bin /data/martin/prosopagnosia/landscapes/Sess01/bold/003/f.nii /data/martin/prosopagnosia/landscapes/Sess01/bold/003/fnew.nii --nskip 3 \n",
      "nskip = 3\n",
      "$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $\n",
      "reading from /data/martin/prosopagnosia/landscapes/Sess01/bold/003/f.nii...\n",
      "TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00\n",
      "i_ras = (-0.999463, -0.0273032, 0.0181267)\n",
      "j_ras = (0.022681, -0.975511, -0.21878)\n",
      "k_ras = (0.0236561, -0.218251, 0.975606)\n",
      "Skipping 3 frames\n",
      "writing to /data/martin/prosopagnosia/landscapes/Sess01/bold/003/fnew.nii...\n"
     ]
    }
   ],
   "source": [
    "expDir=${projectDir}\"landscapes/Sess01/bold/003/\"\n",
    "\n",
    "# make new nifti file \"fnew\" where the first 3 volumes have been dropped\n",
    "mri_convert ${expDir}f.nii ${expDir}fnew.nii --nskip 3\n",
    "\n",
    "# get rid of the original file\n",
    "rm ${expDir}f.nii\n",
    "# name the new file the same way the original file was called\n",
    "mv ${expDir}fnew.nii ${expDir}f.nii"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "mri_convert.bin /data/martin/prosopagnosia/hands/Sess01/bold/005/f.nii /data/martin/prosopagnosia/hands/Sess01/bold/005/fnew.nii --nskip 3 \n",
      "nskip = 3\n",
      "$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $\n",
      "reading from /data/martin/prosopagnosia/hands/Sess01/bold/005/f.nii...\n",
      "TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00\n",
      "i_ras = (-0.999463, -0.0273032, 0.0181267)\n",
      "j_ras = (0.022681, -0.975511, -0.21878)\n",
      "k_ras = (0.0236561, -0.218251, 0.975606)\n",
      "Skipping 3 frames\n",
      "writing to /data/martin/prosopagnosia/hands/Sess01/bold/005/fnew.nii...\n"
     ]
    }
   ],
   "source": [
    "expDir=${projectDir}\"hands/Sess01/bold/005/\"\n",
    "\n",
    "# make new nifti file \"fnew\" where the first 3 volumes have been dropped\n",
    "mri_convert ${expDir}f.nii ${expDir}fnew.nii --nskip 3\n",
    "\n",
    "# get rid of the original file\n",
    "rm ${expDir}f.nii\n",
    "# name the new file the same way the original file was called\n",
    "mv ${expDir}fnew.nii ${expDir}f.nii"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### add meta-information"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "List of sessions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "echo Sess01 > ${projectDir}landscapes/sessids"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Sess01\n"
     ]
    }
   ],
   "source": [
    "cat ${projectDir}landscapes/sessids"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "echo pBrain >  ${projectDir}landscapes/Sess01/subjectname"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "pBrain\n"
     ]
    }
   ],
   "source": [
    "cat ${projectDir}landscapes/Sess01/subjectname"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[34;42m/data/martin/prosopagnosia/landscapes\u001b[00m\n",
      "├── \u001b[34;42mSess01\u001b[00m\n",
      "│   ├── \u001b[34;42mbold\u001b[00m\n",
      "│   │   └── \u001b[34;42m003\u001b[00m\n",
      "│   │       ├── \u001b[01;32mf-infodump.dat\u001b[00m\n",
      "│   │       └── \u001b[01;32mf.nii\u001b[00m\n",
      "│   ├── \u001b[01;32mdcmunpack.log\u001b[00m\n",
      "│   ├── \u001b[01;32mimagelist.dat\u001b[00m\n",
      "│   ├── \u001b[01;32mseries-info.dat\u001b[00m\n",
      "│   └── \u001b[01;32msubjectname\u001b[00m\n",
      "└── \u001b[01;32msessids\u001b[00m\n",
      "\n",
      "3 directories, 7 files\n"
     ]
    }
   ],
   "source": [
    "tree ${projectDir}landscapes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/data/martin/prosopagnosia/\n"
     ]
    }
   ],
   "source": [
    "echo $projectDir"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### preprocessing"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "cd ${projectDir}landscapes"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "preproce-sess:  \n",
    "\n",
    "- sf: File with list of all sessions\n",
    "- surface: name of the subject whos structural data we project on and which hemispheres should be processed\n",
    "- fwhm: level of smoothing\n",
    "- per-run: motion correction within run only (because here we use only one run)\n",
    "- fsd: name of the subdirectory where the functional data are stored"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--------------------------------------------------------------\n",
      "preproc-sess logfile is log/preproc-sess.Sess01.log\n",
      "--------------------------------------------------------------\n",
      "$Id: preproc-sess,v 1.64.2.1 2016/08/02 21:19:09 greve Exp $\n",
      "martin\n",
      "setenv FREESURFER_HOME /usr/local/freesurfer\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "/data/martin/prosopagnosia/landscapes\n",
      "/usr/local/freesurfer/fsfast/bin/preproc-sess\n",
      "-sf sessids -surface pBrain lhrh -fwhm 5 -per-run -fsd bold\n",
      "Fri Nov 24 12:59:30 CET 2017\n",
      "instem   f \n",
      "mc   1     f fmcpr \n",
      "stc  0     fmcpr\n",
      "sm   0   \n",
      "mask 1   brain\n",
      "Sess01 Template -----------------------------\n",
      "mktemplate-sess -s Sess01 -d /data/martin/prosopagnosia/landscapes -fsd bold -update\n",
      " \n",
      "Session: /data/martin/prosopagnosia/landscapes/Sess01 ----------------\n",
      "Fri Nov 24 12:59:30 CET 2017\n",
      "Detected input format at nii\n",
      "/data/martin/prosopagnosia/landscapes\n",
      "mri_convert /data/martin/prosopagnosia/landscapes/Sess01/bold/003/f.nii /data/martin/prosopagnosia/landscapes/Sess01/bold/template.nii.gz --frame 0\n",
      "mri_convert.bin /data/martin/prosopagnosia/landscapes/Sess01/bold/003/f.nii /data/martin/prosopagnosia/landscapes/Sess01/bold/template.nii.gz --frame 0 \n",
      "$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $\n",
      "reading from /data/martin/prosopagnosia/landscapes/Sess01/bold/003/f.nii...\n",
      "TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00\n",
      "i_ras = (-0.999463, -0.0273032, 0.0181267)\n",
      "j_ras = (0.022681, -0.975511, -0.21878)\n",
      "k_ras = (0.0236561, -0.218251, 0.975606)\n",
      "keeping frame 0\n",
      "writing to /data/martin/prosopagnosia/landscapes/Sess01/bold/template.nii.gz...\n",
      "  Run: 003 ----------------\n",
      "  Fri Nov 24 12:59:38 CET 2017\n",
      "/data/martin/prosopagnosia/landscapes\n",
      "mri_convert /data/martin/prosopagnosia/landscapes/Sess01/bold/003/f.nii /data/martin/prosopagnosia/landscapes/Sess01/bold/003/template.nii.gz --mid-frame\n",
      "mri_convert.bin /data/martin/prosopagnosia/landscapes/Sess01/bold/003/f.nii /data/martin/prosopagnosia/landscapes/Sess01/bold/003/template.nii.gz --mid-frame \n",
      "$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $\n",
      "reading from /data/martin/prosopagnosia/landscapes/Sess01/bold/003/f.nii...\n",
      "TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00\n",
      "i_ras = (-0.999463, -0.0273032, 0.0181267)\n",
      "j_ras = (0.022681, -0.975511, -0.21878)\n",
      "k_ras = (0.0236561, -0.218251, 0.975606)\n",
      "keeping frame 83\n",
      "writing to /data/martin/prosopagnosia/landscapes/Sess01/bold/003/template.nii.gz...\n",
      "Fri Nov 24 12:59:45 CET 2017\n",
      "mktemplate-sess completed \n",
      "Sess01 Registration -----------------------------\n",
      "register-sess -s Sess01 -d /data/martin/prosopagnosia/landscapes -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg\n",
      "--------------------------------------------------------------\n",
      "register-sess logfile is /data/martin/prosopagnosia/landscapes/log/register-sess.Sess01.log\n",
      "--------------------------------------------------------------\n",
      "Fri Nov 24 12:59:45 CET 2017\n",
      "\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/landscapes\n",
      "/usr/local/freesurfer/fsfast/bin/register-sess -s Sess01 -d /data/martin/prosopagnosia/landscapes -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg\n",
      "\n",
      "freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      " \n",
      "Session: /data/martin/prosopagnosia/landscapes/Sess01 ----------------\n",
      "Fri Nov 24 12:59:45 CET 2017\n",
      "--------------------------------------\n",
      "/data/martin/prosopagnosia/landscapes/Sess01\n",
      "bbregister --s pBrain --init-coreg --6 --bold --mov bold/template.nii.gz --reg bold/register.dof6.dat --lta bold/register.dof6.lta --init-reg-out bold/init.register.dof6.dat\n",
      "tmp bold/tmp.bbregister.22861\n",
      "Log file is bold/register.dof6.dat.log\n",
      "Fri Nov 24 12:59:45 CET 2017\n",
      "\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/landscapes/Sess01\n",
      "/usr/local/freesurfer/bin/bbregister --s pBrain --init-coreg --6 --bold --mov bold/template.nii.gz --reg bold/register.dof6.dat --lta bold/register.dof6.lta --init-reg-out bold/init.register.dof6.dat\n",
      "\n",
      "$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "FREESURFER_HOME /usr/local/freesurfer\n",
      "mri_convert bold/template.nii.gz bold/tmp.bbregister.22861/template.nii\n",
      "mri_convert.bin bold/template.nii.gz bold/tmp.bbregister.22861/template.nii \n",
      "$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $\n",
      "reading from bold/template.nii.gz...\n",
      "TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00\n",
      "i_ras = (-0.999463, -0.0273032, 0.0181267)\n",
      "j_ras = (0.022681, -0.975511, -0.21878)\n",
      "k_ras = (0.0236561, -0.218251, 0.975606)\n",
      "writing to bold/tmp.bbregister.22861/template.nii...\n",
      "mri_coreg --s pBrain --mov bold/tmp.bbregister.22861/template.nii --regdat bold/tmp.bbregister.22861/reg.init.dat --reg bold/tmp.bbregister.22861/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01\n",
      "\n",
      "$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/landscapes/Sess01\n",
      "cmdline mri_coreg --s pBrain --mov bold/tmp.bbregister.22861/template.nii --regdat bold/tmp.bbregister.22861/reg.init.dat --reg bold/tmp.bbregister.22861/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "dof    6\n",
      "nsep    1\n",
      "cras0    1\n",
      "ftol    0.000100\n",
      "linmintol    0.010000\n",
      "bf       1\n",
      "bflim    30.000000\n",
      "bfnsamp    30\n",
      "SmoothRef 0\n",
      "SatPct    99.990000\n",
      "MovOOB 0\n",
      "optschema 1\n",
      "Reading in mov bold/tmp.bbregister.22861/template.nii\n",
      "Reading in ref /usr/local/freesurfer/subjects/pBrain/mri/brainmask.mgz\n",
      "Reading in and applying refmask /usr/local/freesurfer/subjects/pBrain/mri/aparc+aseg.mgz\n",
      "Setting cras translation parameters to align centers\n",
      "Creating random numbers for coordinate dithering\n",
      "Performing intensity dithering\n",
      "Initial parameters  4.8266 -14.2690  7.8386  0.0000  0.0000  0.0000  1.0000  1.0000  1.0000  0.0000  0.0000  0.0000 \n",
      "Separation list (1):  4   min = 4\n",
      "DoSmoothing 1\n",
      "DoCoordDither 1\n",
      "DoIntensityDither 1\n",
      "nitersmax 4\n",
      "ftol 1.000e-04\n",
      "linmintol 1.000e-02\n",
      "SatPct 99.990000\n",
      "Hist FWHM 7.000000 7.000000\n",
      "nthreads 1\n",
      "movsat = 1668.0000\n",
      "mov gstd 1.6917 1.6917 1.6917\n",
      "Smoothing mov\n",
      "refsat = 115.0000\n",
      "ref gstd 1.8914 1.8914 1.8914\n",
      "Smoothing ref\n",
      "COREGpreproc() done\n",
      "Testing if mov and target overlap\n",
      "Init cost   -1.0419184735\n",
      "nhits = 78038 out of 16777216, Percent Overlap:  29.8\n",
      "Initial  RefRAS-to-MovRAS\n",
      " 1.00000   0.00000   0.00000   4.82664;\n",
      " 0.00000   1.00000   0.00000  -14.26899;\n",
      " 0.00000   0.00000   1.00000   7.83862;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Initial  RefVox-to-MovVox\n",
      " 0.49973  -0.00906  -0.01365   2.68039;\n",
      "-0.01134   0.10939  -0.48776   113.18749;\n",
      "-0.01183  -0.48780  -0.10913   97.11647;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "sep = 4 -----------------------------------\n",
      "COREGoptBruteForce() 30 1 30\n",
      "Turning on MovOOB for BruteForce Search\n",
      "#BF# sep= 4 iter=0 lim=30.0 delta=2.00   4.82664  -0.26899 -10.16138   2.00000   0.00000   0.00000   -1.0316124\n",
      "Turning  MovOOB back off after brute force search\n",
      "\n",
      "\n",
      "---------------------------------\n",
      "Init Powel Params dof = 6\n",
      "Starting OpenPowel2(), sep = 4\n",
      "InitialCost        -1.0702683926 \n",
      "#@#  4  188  4.82664 -0.26899 -10.16138 2.00000 0.00000 0.00000   -1.0702684\n",
      "fs_powell::minimize\n",
      "  nparams 6\n",
      "  maxfev 4\n",
      "  ftol   0.000100\n",
      "  linmin_xtol_   0.010000\n",
      "  powell nthiter 0: fret = -1.070268\n",
      "#@#  4  195  4.69693 -0.26899 -10.16138 2.00000 0.00000 0.00000   -1.0702726\n",
      "#@#  4  196  4.70693 -0.26899 -10.16138 2.00000 0.00000 0.00000   -1.0702729\n",
      "#@#  4  201  4.70693 -1.88702 -10.16138 2.00000 0.00000 0.00000   -1.0724304\n",
      "#@#  4  204  4.70693 -5.39074 -10.16138 2.00000 0.00000 0.00000   -1.0725826\n",
      "#@#  4  206  4.70693 -3.71356 -10.16138 2.00000 0.00000 0.00000   -1.0734887\n",
      "#@#  4  207  4.70693 -3.70356 -10.16138 2.00000 0.00000 0.00000   -1.0734893\n",
      "#@#  4  212  4.70693 -3.70356 -9.16138 2.00000 0.00000 0.00000   -1.0740371\n",
      "#@#  4  215  4.70693 -3.70356 -8.54335 2.00000 0.00000 0.00000   -1.0740403\n",
      "#@#  4  217  4.70693 -3.70356 -8.84549 2.00000 0.00000 0.00000   -1.0740680\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "#@#  4  218  4.70693 -3.70356 -8.83549 2.00000 0.00000 0.00000   -1.0740755\n",
      "#@#  4  220  4.70693 -3.70356 -8.78766 2.00000 0.00000 0.00000   -1.0740772\n",
      "#@#  4  225  4.70693 -3.70356 -8.78766 0.38197 0.00000 0.00000   -1.0743752\n",
      "#@#  4  226  4.70693 -3.70356 -8.78766 0.80065 0.00000 0.00000   -1.0744169\n",
      "#@#  4  229  4.70693 -3.70356 -8.78766 0.97563 0.00000 0.00000   -1.0744258\n",
      "#@#  4  230  4.70693 -3.70356 -8.78766 0.93414 0.00000 0.00000   -1.0744308\n",
      "#@#  4  235  4.70693 -3.70356 -8.78766 0.93414 1.00000 0.00000   -1.0745195\n",
      "#@#  4  239  4.70693 -3.70356 -8.78766 0.93414 0.61803 0.00000   -1.0745244\n",
      "#@#  4  240  4.70693 -3.70356 -8.78766 0.93414 0.76267 0.00000   -1.0745360\n",
      "#@#  4  242  4.70693 -3.70356 -8.78766 0.93414 0.70573 0.00000   -1.0745387\n",
      "#@#  4  244  4.70693 -3.70356 -8.78766 0.93414 0.72713 0.00000   -1.0745389\n",
      "#@#  4  248  4.70693 -3.70356 -8.78766 0.93414 0.72713 1.00000   -1.0746741\n",
      "#@#  4  252  4.70693 -3.70356 -8.78766 0.93414 0.72713 0.61803   -1.0747194\n",
      "#@#  4  253  4.70693 -3.70356 -8.78766 0.93414 0.72713 0.63632   -1.0747211\n",
      "  powell nthiter 1: fret = -1.074721\n",
      "#@#  4  263  5.08889 -3.70356 -8.78766 0.93414 0.72713 0.63632   -1.0747627\n",
      "#@#  4  264  4.97620 -3.70356 -8.78766 0.93414 0.72713 0.63632   -1.0747694\n",
      "#@#  4  265  4.98620 -3.70356 -8.78766 0.93414 0.72713 0.63632   -1.0747709\n",
      "#@#  4  274  4.98620 -3.69356 -8.78766 0.93414 0.72713 0.63632   -1.0747725\n",
      "#@#  4  283  4.98620 -3.69356 -8.40570 0.93414 0.72713 0.63632   -1.0748479\n",
      "#@#  4  284  4.98620 -3.69356 -8.35464 0.93414 0.72713 0.63632   -1.0748602\n",
      "#@#  4  286  4.98620 -3.69356 -8.29090 0.93414 0.72713 0.63632   -1.0748610\n",
      "#@#  4  290  4.98620 -3.69356 -8.30181 0.93414 0.72713 0.63632   -1.0748625\n",
      "#@#  4  297  4.98620 -3.69356 -8.30181 0.67278 0.72713 0.63632   -1.0748709\n",
      "#@#  4  300  4.98620 -3.69356 -8.30181 0.80427 0.72713 0.63632   -1.0748734\n",
      "#@#  4  302  4.98620 -3.69356 -8.30181 0.79135 0.72713 0.63632   -1.0748740\n",
      "#@#  4  321  4.98620 -3.69356 -8.30181 0.79135 0.72713 1.01829   -1.0749249\n",
      "#@#  4  324  4.98620 -3.69356 -8.30181 0.79135 0.72713 1.00829   -1.0749264\n",
      "  powell nthiter 2: fret = -1.074926\n",
      "#@#  4  331  5.36817 -3.69356 -8.30181 0.79135 0.72713 1.00829   -1.0749667\n",
      "#@#  4  332  5.25982 -3.69356 -8.30181 0.79135 0.72713 1.00829   -1.0749801\n",
      "#@#  4  350  5.25982 -3.68356 -8.28238 0.79135 0.72713 1.00829   -1.0749803\n",
      "#@#  4  370  5.25982 -3.68356 -8.28238 0.79135 0.79652 1.00829   -1.0749838\n",
      "#@#  4  371  5.25982 -3.68356 -8.28238 0.79135 0.80710 1.00829   -1.0749866\n",
      "#@#  4  380  5.25982 -3.68356 -8.28238 0.79135 0.80710 1.39025   -1.0749960\n",
      "#@#  4  381  5.25982 -3.68356 -8.28238 0.79135 0.80710 1.22360   -1.0750051\n",
      "#@#  4  382  5.25982 -3.68356 -8.28238 0.79135 0.80710 1.23360   -1.0750053\n",
      "#@#  4  383  5.25982 -3.68356 -8.28238 0.79135 0.80710 1.25248   -1.0750074\n",
      "Powell done niters total = 2\n",
      "OptTimeSec  8.0 sec\n",
      "OptTimeMin  0.13 min\n",
      "nEvals 385\n",
      "Final parameters   5.25981998  -3.68355894  -8.28238297   0.79134727   0.80710346   1.25247550 \n",
      "Final cost   -1.075007492400009\n",
      " \n",
      "\n",
      "---------------------------------\n",
      "mri_coreg utimesec    46.508000\n",
      "mri_coreg stimesec    0.124000\n",
      "mri_coreg ru_maxrss   427092\n",
      "mri_coreg ru_ixrss    0\n",
      "mri_coreg ru_idrss    0\n",
      "mri_coreg ru_isrss    0\n",
      "mri_coreg ru_minflt   126905\n",
      "mri_coreg ru_majflt   0\n",
      "mri_coreg ru_nswap    0\n",
      "mri_coreg ru_inblock  0\n",
      "mri_coreg ru_oublock  0\n",
      "mri_coreg ru_msgsnd   0\n",
      "mri_coreg ru_msgrcv   0\n",
      "mri_coreg ru_nsignals 0\n",
      "mri_coreg ru_nvcsw    46\n",
      "mri_coreg ru_nivcsw   82\n",
      "Final  RefRAS-to-MovRAS\n",
      " 0.99966   0.02186   0.01409   5.25982;\n",
      "-0.02205   0.99966   0.01381  -3.68356;\n",
      "-0.01378  -0.01412   0.99981  -8.28238;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Final  RefVox-to-MovVox\n",
      " 0.49939  -0.00183  -0.02470   2.82339;\n",
      "-0.02360   0.11594  -0.48580   110.36914;\n",
      "-0.00751  -0.48637  -0.11572   88.23644;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Final parameters  5.2598 -3.6836 -8.2824  0.7913  0.8071  1.2525 \n",
      "nhits = 75838 out of 16777216, Percent Overlap:  28.9\n",
      "mri_coreg RunTimeSec 46.6 sec\n",
      "To check run:\n",
      "   tkregisterfv --mov bold/tmp.bbregister.22861/template.nii --targ /usr/local/freesurfer/subjects/pBrain/mri/brainmask.mgz --reg bold/tmp.bbregister.22861/mri_coreg.lta --s pBrain --surfs \n",
      "\n",
      "mri_coreg done\n",
      "\n",
      "mri_segreg --mov bold/tmp.bbregister.22861/template.nii --init-reg bold/tmp.bbregister.22861/reg.init.dat --out-reg bold/tmp.bbregister.22861/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5\n",
      "$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/landscapes/Sess01\n",
      "mri_segreg --mov bold/tmp.bbregister.22861/template.nii --init-reg bold/tmp.bbregister.22861/reg.init.dat --out-reg bold/tmp.bbregister.22861/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "movvol bold/tmp.bbregister.22861/template.nii\n",
      "regfile bold/tmp.bbregister.22861/reg.init.dat\n",
      "subject pBrain\n",
      "dof 6\n",
      "outregfile bold/tmp.bbregister.22861/bbr.pass1.dat\n",
      "UseMask 0\n",
      "UseLH 1\n",
      "UseRH 1\n",
      "nsubsamp 100\n",
      "PenaltySign  -1\n",
      "PenaltySlope 0.500000\n",
      "PenaltyCenter 0.000000\n",
      "surfname white\n",
      "GMProjFrac 0.500000\n",
      "WMProjAbs 2.000000\n",
      "lhcostfile (null)\n",
      "rhcostfile (null)\n",
      "interp  trilinear (1)\n",
      "frame  0\n",
      "TolPowell 0.000100\n",
      "nMaxItersPowell 36\n",
      "n1dmin  3\n",
      "Profile   0\n",
      "Gdiag_no  -1\n",
      "AddNoise  0 (0)\n",
      "SynthSeed 1511580580\n",
      "TransRandMax 0.000000\n",
      "RotRandMax 0.000000\n",
      "Translations 0.000000 0.000000 0.000000\n",
      "Rotations   0.000000 0.000000 0.000000\n",
      "Input reg\n",
      " 0.99877   0.04939  -0.00367   1.30222;\n",
      " 0.01502  -0.23143   0.97274  -19.58270;\n",
      "-0.04720   0.97160   0.23189   7.98565;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Loading mov\n",
      "Projecting LH Surfs\n",
      "Loading lh.white surf\n",
      "Loading lh.thickness for GM\n",
      "GM Proj: 1 0.500000 2.000000\n",
      "WM Proj: 0 0.500000 2.000000\n",
      "Projecting RH Surfs\n",
      "Loading rh.white surf\n",
      "Loading rh.thickness for GM\n",
      "Projecting RH Surfs\n",
      "Using lh.cortex.label\n",
      "Using rh.cortex.label\n",
      "Computing relative cost\n",
      " 0  -25.0 -25.0 -25.0   0.990295\n",
      " 1  -25.0 -25.0  25.0   1.038852\n",
      " 2  -25.0  25.0 -25.0   1.023949\n",
      " 3  -25.0  25.0  25.0   0.984337\n",
      " 4   25.0 -25.0 -25.0   1.056613\n",
      " 5   25.0 -25.0  25.0   1.086173\n",
      " 6   25.0  25.0 -25.0   1.050580\n",
      " 7   25.0  25.0  25.0   1.058504\n",
      "REL:  8  0.572608    8.289302  1.036163 rel = 0.552624 \n",
      "Initial costs ----------------\n",
      "Number of surface hits 1619\n",
      "WM  Intensity   770.0277 +/- 108.5384\n",
      "Ctx Intensity   820.7734 +/- 158.6266\n",
      "Pct Contrast      4.8150 +/-  21.8763\n",
      "Cost   0.5726\n",
      "RelCost   0.5526\n",
      "\n",
      "------------------------------------\n",
      "Brute force preopt -4 4 4, n = 729\n",
      "     0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      1.0930   1.0930  0.0\n",
      "     1  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   0.0000      1.0701   1.0701  0.0\n",
      "     3  -4.0000  -4.0000  -4.0000  -4.0000   0.0000  -4.0000      1.0354   1.0354  0.0\n",
      "     4  -4.0000  -4.0000  -4.0000  -4.0000   0.0000   0.0000      1.0350   1.0350  0.0\n",
      "     5  -4.0000  -4.0000  -4.0000  -4.0000   0.0000   4.0000      1.0281   1.0281  0.0\n",
      "     6  -4.0000  -4.0000  -4.0000  -4.0000   4.0000  -4.0000      0.9473   0.9473  0.0\n",
      "    15  -4.0000  -4.0000  -4.0000   0.0000   4.0000  -4.0000      0.9362   0.9362  0.0\n",
      "    45  -4.0000  -4.0000   0.0000   4.0000  -4.0000  -4.0000      0.9260   0.9260  0.0\n",
      "    46  -4.0000  -4.0000   0.0000   4.0000  -4.0000   0.0000      0.9153   0.9153  0.0\n",
      "   106  -4.0000   0.0000  -4.0000   4.0000   4.0000   0.0000      0.9029   0.9029  0.0\n",
      "   117  -4.0000   0.0000   0.0000   0.0000  -4.0000  -4.0000      0.8908   0.8908  0.0\n",
      "   118  -4.0000   0.0000   0.0000   0.0000  -4.0000   0.0000      0.8477   0.8477  0.0\n",
      "   265   0.0000  -4.0000  -4.0000   4.0000   0.0000   0.0000      0.8441   0.8441  0.0\n",
      "   292   0.0000  -4.0000   0.0000   4.0000   0.0000   0.0000      0.7653   0.7653  0.0\n",
      "   337   0.0000   0.0000  -4.0000   0.0000   0.0000   0.0000      0.7166   0.7166  0.0\n",
      "   346   0.0000   0.0000  -4.0000   4.0000   0.0000   0.0000      0.7114   0.7114  0.0\n",
      "   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.5726   0.5726  0.0\n",
      "Brute Force --------------------------\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Min cost was 0.572608\n",
      "Number of iterations   729\n",
      "Search time 0.642000 sec\n",
      "Parameters at best (transmm, rotdeg)\n",
      "  0.000   0.000   0.000  0.000  0.000  0.000 \n",
      "--------------------------------------------\n",
      "\n",
      "Starting Powell Minimization\n",
      "Init Powel Params dof = 6\n",
      "0 0\n",
      "1 0\n",
      "2 0\n",
      "3 0\n",
      "4 0\n",
      "5 0\n",
      "fs_powell::minimize\n",
      "  nparams 6\n",
      "  maxfev 36\n",
      "  ftol   0.000100\n",
      "  linmin_xtol_   0.001000\n",
      "  powell nthiter 0: fret = 0.572608\n",
      "   6  0.382  0.000  0.000  0.000  0.000  0.000   0.5724392174\n",
      "   7  0.194  0.000  0.000  0.000  0.000  0.000   0.5709779751\n",
      "   8  0.196  0.000  0.000  0.000  0.000  0.000   0.5709692942\n",
      "   9  0.230  0.000  0.000  0.000  0.000  0.000   0.5709151806\n",
      "  11  0.222  0.000  0.000  0.000  0.000  0.000   0.5709056186\n",
      "  13  0.223  0.000  0.000  0.000  0.000  0.000   0.5709056157\n",
      "  14  0.224  0.000  0.000  0.000  0.000  0.000   0.5709055502\n",
      "  19  0.224 -1.618  0.000  0.000  0.000  0.000   0.5638383516\n",
      "  20  0.224 -0.855  0.000  0.000  0.000  0.000   0.5404951102\n",
      "  24  0.224 -0.833  0.000  0.000  0.000  0.000   0.5403749150\n",
      "  25  0.224 -0.807  0.000  0.000  0.000  0.000   0.5400161640\n",
      "  26  0.224 -0.701  0.000  0.000  0.000  0.000   0.5394375264\n",
      "  30  0.224 -0.699  0.000  0.000  0.000  0.000   0.5394219016\n",
      "  31  0.224 -0.691  0.000  0.000  0.000  0.000   0.5394207790\n",
      "  33  0.224 -0.695  0.000  0.000  0.000  0.000   0.5394115431\n",
      "  38  0.224 -0.695 -1.618  0.000  0.000  0.000   0.4766896146\n",
      "  39  0.224 -0.695 -1.518  0.000  0.000  0.000   0.4763573949\n",
      "  44  0.224 -0.695 -1.484  0.000  0.000  0.000   0.4762369559\n",
      "  45  0.224 -0.695 -1.481  0.000  0.000  0.000   0.4762329612\n",
      "  46  0.224 -0.695 -1.472  0.000  0.000  0.000   0.4762315489\n",
      "  48  0.224 -0.695 -1.475  0.000  0.000  0.000   0.4762301881\n",
      "  52  0.224 -0.695 -1.475  1.000  0.000  0.000   0.4441232838\n",
      "  56  0.224 -0.695 -1.475  0.618  0.000  0.000   0.4440997870\n",
      "  57  0.224 -0.695 -1.475  0.809  0.000  0.000   0.4427901338\n",
      "  59  0.224 -0.695 -1.475  0.882  0.000  0.000   0.4422571725\n",
      "  61  0.224 -0.695 -1.475  0.875  0.000  0.000   0.4421965646\n",
      "  63  0.224 -0.695 -1.475  0.865  0.000  0.000   0.4421182190\n",
      "  66  0.224 -0.695 -1.475  0.863  0.000  0.000   0.4421014320\n",
      "  67  0.224 -0.695 -1.475  0.861  0.000  0.000   0.4420925469\n",
      "  73  0.224 -0.695 -1.475  0.861 -0.618  0.000   0.4232318573\n",
      "  76  0.224 -0.695 -1.475  0.861 -0.629  0.000   0.4230217373\n",
      "  78  0.224 -0.695 -1.475  0.861 -0.672  0.000   0.4226371003\n",
      "  80  0.224 -0.695 -1.475  0.861 -0.671  0.000   0.4226368228\n",
      "  88  0.224 -0.695 -1.475  0.861 -0.671 -0.006   0.4224454045\n",
      "  94  0.224 -0.695 -1.475  0.861 -0.671 -0.003   0.4224198684\n",
      "  95  0.224 -0.695 -1.475  0.861 -0.671 -0.002   0.4224037561\n",
      "  96  0.224 -0.695 -1.475  0.861 -0.671 -0.001   0.4223921692\n",
      "  powell nthiter 1: fret = 0.422392\n",
      " 104 -0.071 -0.695 -1.475  0.861 -0.671 -0.001   0.4185434711\n",
      " 106 -0.194 -0.695 -1.475  0.861 -0.671 -0.001   0.4173570124\n",
      " 107 -0.167 -0.695 -1.475  0.861 -0.671 -0.001   0.4173507424\n",
      " 108 -0.179 -0.695 -1.475  0.861 -0.671 -0.001   0.4173340726\n",
      " 117 -0.178 -1.313 -1.475  0.861 -0.671 -0.001   0.3892848470\n",
      " 121 -0.178 -1.323 -1.475  0.861 -0.671 -0.001   0.3888679376\n",
      " 122 -0.178 -1.363 -1.475  0.861 -0.671 -0.001   0.3885148251\n",
      " 124 -0.178 -1.355 -1.475  0.861 -0.671 -0.001   0.3883929809\n",
      " 125 -0.178 -1.349 -1.475  0.861 -0.671 -0.001   0.3883301150\n",
      " 127 -0.178 -1.345 -1.475  0.861 -0.671 -0.001   0.3883039277\n",
      " 137 -0.178 -1.345 -1.434  0.861 -0.671 -0.001   0.3870489873\n",
      " 138 -0.178 -1.345 -1.350  0.861 -0.671 -0.001   0.3867874746\n",
      " 140 -0.178 -1.345 -1.385  0.861 -0.671 -0.001   0.3867198421\n",
      " 141 -0.178 -1.345 -1.377  0.861 -0.671 -0.001   0.3866859104\n",
      " 142 -0.178 -1.345 -1.371  0.861 -0.671 -0.001   0.3866810591\n",
      " 144 -0.178 -1.345 -1.370  0.861 -0.671 -0.001   0.3866810170\n",
      " 152 -0.178 -1.345 -1.370  1.243 -0.671 -0.001   0.3860971240\n",
      " 153 -0.178 -1.345 -1.370  1.060 -0.671 -0.001   0.3830333138\n",
      " 156 -0.178 -1.345 -1.370  1.053 -0.671 -0.001   0.3830230446\n",
      " 157 -0.178 -1.345 -1.370  1.052 -0.671 -0.001   0.3830229855\n",
      " 166 -0.178 -1.345 -1.370  1.052 -0.735 -0.001   0.3825248156\n",
      " 171 -0.178 -1.345 -1.370  1.052 -0.731 -0.001   0.3825187521\n",
      " 174 -0.178 -1.345 -1.370  1.052 -0.730 -0.001   0.3825187020\n",
      " 181 -0.178 -1.345 -1.370  1.052 -0.730 -0.091   0.3808053901\n",
      " 183 -0.178 -1.345 -1.370  1.052 -0.730 -0.170   0.3796473662\n",
      " 190 -0.178 -1.345 -1.370  1.052 -0.730 -0.172   0.3796440541\n",
      "  powell nthiter 2: fret = 0.379644\n",
      " 199 -0.145 -1.345 -1.370  1.052 -0.730 -0.172   0.3793230316\n",
      " 201 -0.151 -1.345 -1.370  1.052 -0.730 -0.172   0.3793053580\n",
      " 203 -0.150 -1.345 -1.370  1.052 -0.730 -0.172   0.3793053206\n",
      " 214 -0.150 -1.335 -1.370  1.052 -0.730 -0.172   0.3792467669\n",
      " 218 -0.150 -1.336 -1.370  1.052 -0.730 -0.172   0.3792439951\n",
      " 227 -0.150 -1.336 -1.402  1.052 -0.730 -0.172   0.3786949433\n",
      " 228 -0.150 -1.336 -1.424  1.052 -0.730 -0.172   0.3786160185\n",
      " 229 -0.150 -1.336 -1.419  1.052 -0.730 -0.172   0.3786136892\n",
      " 238 -0.150 -1.336 -1.419  1.040 -0.730 -0.172   0.3785037911\n",
      " 239 -0.150 -1.336 -1.419  1.006 -0.730 -0.172   0.3785032243\n",
      " 241 -0.150 -1.336 -1.419  1.022 -0.730 -0.172   0.3784235700\n",
      " 243 -0.150 -1.336 -1.419  1.020 -0.730 -0.172   0.3784202161\n",
      " 246 -0.150 -1.336 -1.419  1.019 -0.730 -0.172   0.3784194217\n",
      " 253 -0.150 -1.336 -1.419  1.019 -0.691 -0.172   0.3781716742\n",
      " 255 -0.150 -1.336 -1.419  1.019 -0.700 -0.172   0.3781538142\n",
      " 256 -0.150 -1.336 -1.419  1.019 -0.699 -0.172   0.3781514499\n",
      " 257 -0.150 -1.336 -1.419  1.019 -0.697 -0.172   0.3781506869\n",
      " 265 -0.150 -1.336 -1.419  1.019 -0.697 -0.162   0.3781432843\n",
      " 267 -0.150 -1.336 -1.419  1.019 -0.697 -0.164   0.3781424833\n",
      "  powell nthiter 3: fret = 0.378142\n",
      " 278 -0.146 -1.336 -1.419  1.019 -0.697 -0.164   0.3781341805\n",
      " 290 -0.146 -1.333 -1.419  1.019 -0.697 -0.164   0.3781319888\n",
      " 292 -0.146 -1.334 -1.419  1.019 -0.697 -0.164   0.3781310881\n",
      " 303 -0.146 -1.334 -1.417  1.019 -0.697 -0.164   0.3781276810\n",
      " 305 -0.146 -1.334 -1.415  1.019 -0.697 -0.164   0.3781275965\n",
      " 307 -0.146 -1.334 -1.416  1.019 -0.697 -0.164   0.3781271823\n",
      " 315 -0.146 -1.334 -1.416  1.024 -0.697 -0.164   0.3781197196\n",
      " 326 -0.146 -1.334 -1.416  1.024 -0.700 -0.164   0.3781185367\n",
      " 327 -0.146 -1.334 -1.416  1.024 -0.699 -0.164   0.3781182879\n",
      " 334 -0.146 -1.334 -1.416  1.024 -0.699 -0.161   0.3781154933\n",
      " 336 -0.146 -1.334 -1.416  1.024 -0.699 -0.159   0.3781153924\n",
      " 337 -0.146 -1.334 -1.416  1.024 -0.699 -0.158   0.3781152786\n",
      "Powell done niters = 3\n",
      "Computing relative cost\n",
      " 0  -25.0 -25.0 -25.0   1.017047\n",
      " 1  -25.0 -25.0  25.0   1.015377\n",
      " 2  -25.0  25.0 -25.0   1.003295\n",
      " 3  -25.0  25.0  25.0   1.003003\n",
      " 4   25.0 -25.0 -25.0   1.019897\n",
      " 5   25.0 -25.0  25.0   1.048078\n",
      " 6   25.0  25.0 -25.0   1.099154\n",
      " 7   25.0  25.0  25.0   1.031606\n",
      "REL:  8  0.378115    8.237457  1.029682 rel = 0.367216 \n",
      "Number of iterations     3\n",
      "Min cost was 0.378115\n",
      "Number of FunctionCalls   338\n",
      "TolPowell 0.000100\n",
      "nMaxItersPowell 36\n",
      "OptimizationTime 0.328000 sec\n",
      "Parameters at optimum (transmm) -0.14605 -1.33384 -1.41604\n",
      "Parameters at optimum (rotdeg)  1.02366 -0.69906 -0.15839 \n",
      "Final costs ----------------\n",
      "Number of surface hits 1660\n",
      "WM  Intensity   744.5744 +/- 118.3039\n",
      "Ctx Intensity   822.8611 +/- 171.9620\n",
      "Pct Contrast      8.2788 +/-  22.6604\n",
      "Cost   0.3781\n",
      "RelCost   0.5526\n",
      "Reg at min cost was \n",
      " 0.99931   0.03690  -0.00403   1.00841;\n",
      " 0.01310  -0.24886   0.96845  -21.05935;\n",
      "-0.03473   0.96784   0.24917   6.23380;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Writing optimal reg to bold/tmp.bbregister.22861/bbr.pass1.dat, type = 14 \n",
      "Original Reg \n",
      " 0.99877   0.04939  -0.00367   1.30222;\n",
      " 0.01502  -0.23143   0.97274  -19.58270;\n",
      "-0.04720   0.97160   0.23189   7.98565;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Original Reg - Optimal Reg\n",
      "-0.00054   0.01249   0.00036   0.29382;\n",
      " 0.00192   0.01742   0.00428   1.47664;\n",
      "-0.01246   0.00376  -0.01728   1.75185;\n",
      " 0.00000   0.00000   0.00000   0.00000;\n",
      "\n",
      "Computing change in lh position\n",
      "LH rmsDiffMean 1.909965\n",
      "Computing change in rh position\n",
      "Surface-RMS-Diff-mm 1.771856 0.539385 3.135483\n",
      "mri_segreg done\n",
      "mri_segreg --mov bold/tmp.bbregister.22861/template.nii --init-reg bold/tmp.bbregister.22861/bbr.pass1.dat --out-reg bold/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/tmp.bbregister.22861/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/landscapes/Sess01\n",
      "mri_segreg --mov bold/tmp.bbregister.22861/template.nii --init-reg bold/tmp.bbregister.22861/bbr.pass1.dat --out-reg bold/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/tmp.bbregister.22861/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "movvol bold/tmp.bbregister.22861/template.nii\n",
      "regfile bold/tmp.bbregister.22861/bbr.pass1.dat\n",
      "subject pBrain\n",
      "dof 6\n",
      "outregfile bold/register.dof6.dat\n",
      "UseMask 0\n",
      "UseLH 1\n",
      "UseRH 1\n",
      "nsubsamp 1\n",
      "PenaltySign  -1\n",
      "PenaltySlope 0.500000\n",
      "PenaltyCenter 0.000000\n",
      "surfname white\n",
      "GMProjFrac 0.500000\n",
      "WMProjAbs 2.000000\n",
      "lhcostfile (null)\n",
      "rhcostfile (null)\n",
      "interp  trilinear (1)\n",
      "frame  0\n",
      "TolPowell 0.000000\n",
      "nMaxItersPowell 36\n",
      "n1dmin  3\n",
      "Profile   0\n",
      "Gdiag_no  -1\n",
      "AddNoise  0 (0)\n",
      "SynthSeed 1511830665\n",
      "TransRandMax 0.000000\n",
      "RotRandMax 0.000000\n",
      "Translations 0.000000 0.000000 0.000000\n",
      "Rotations   0.000000 0.000000 0.000000\n",
      "Input reg\n",
      " 0.99931   0.03690  -0.00403   1.00841;\n",
      " 0.01310  -0.24886   0.96845  -21.05935;\n",
      "-0.03473   0.96784   0.24917   6.23380;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Loading mov\n",
      "Projecting LH Surfs\n",
      "Loading lh.white surf\n",
      "Loading lh.thickness for GM\n",
      "GM Proj: 1 0.500000 2.000000\n",
      "WM Proj: 0 0.500000 2.000000\n",
      "Projecting RH Surfs\n",
      "Loading rh.white surf\n",
      "Loading rh.thickness for GM\n",
      "Projecting RH Surfs\n",
      "Using lh.cortex.label\n",
      "Using rh.cortex.label\n",
      "Computing relative cost\n",
      " 0  -25.0 -25.0 -25.0   1.008937\n",
      " 1  -25.0 -25.0  25.0   1.018808\n",
      " 2  -25.0  25.0 -25.0   1.037293\n",
      " 3  -25.0  25.0  25.0   1.019545\n",
      " 4   25.0 -25.0 -25.0   1.016638\n",
      " 5   25.0 -25.0  25.0   1.031685\n",
      " 6   25.0  25.0 -25.0   1.037606\n",
      " 7   25.0  25.0  25.0   1.023393\n",
      "REL:  8  0.382066    8.193906  1.024238 rel = 0.373024 \n",
      "Initial costs ----------------\n",
      "Number of surface hits 165444\n",
      "WM  Intensity   744.1139 +/- 121.3909\n",
      "Ctx Intensity   824.0023 +/- 170.1429\n",
      "Pct Contrast      8.6119 +/-  22.1076\n",
      "Cost   0.3821\n",
      "RelCost   0.3730\n",
      "\n",
      "------------------------------------\n",
      "Brute force preopt -0.1 0.1 0.1, n = 729\n",
      "     0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.3892   0.3892  0.0\n",
      "     1  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000   0.0000      0.3866   0.3866  0.0\n",
      "     2  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000   0.1000      0.3852   0.3852  0.0\n",
      "    10  -0.1000  -0.1000  -0.1000   0.0000  -0.1000   0.0000      0.3842   0.3842  0.0\n",
      "    11  -0.1000  -0.1000  -0.1000   0.0000  -0.1000   0.1000      0.3834   0.3834  0.0\n",
      "    82  -0.1000   0.0000  -0.1000  -0.1000  -0.1000   0.0000      0.3830   0.3830  0.0\n",
      "    83  -0.1000   0.0000  -0.1000  -0.1000  -0.1000   0.1000      0.3828   0.3828  0.0\n",
      "    90  -0.1000   0.0000  -0.1000   0.0000  -0.1000  -0.1000      0.3827   0.3827  0.0\n",
      "    91  -0.1000   0.0000  -0.1000   0.0000  -0.1000   0.0000      0.3797   0.3797  0.0\n",
      "   121  -0.1000   0.0000   0.0000   0.0000   0.0000   0.0000      0.3794   0.3794  0.0\n",
      "   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.3781   0.3781  0.0\n",
      "Brute Force --------------------------\n",
      "Min cost was 0.378115\n",
      "Number of iterations   729\n",
      "Search time 0.608000 sec\n",
      "Parameters at best (transmm, rotdeg)\n",
      "  0.000   0.000   0.000  0.000  0.000  0.000 \n",
      "--------------------------------------------\n",
      "\n",
      "Starting Powell Minimization\n",
      "Init Powel Params dof = 6\n",
      "0 0\n",
      "1 0\n",
      "2 0\n",
      "3 0\n",
      "4 0\n",
      "5 0\n",
      "fs_powell::minimize\n",
      "  nparams 6\n",
      "  maxfev 36\n",
      "  ftol   0.000000\n",
      "  linmin_xtol_   0.001000\n",
      "  powell nthiter 0: fret = 0.382066\n",
      "   7  0.068  0.000  0.000  0.000  0.000  0.000   0.3818184021\n",
      "   8  0.061  0.000  0.000  0.000  0.000  0.000   0.3818109576\n",
      "   9  0.057  0.000  0.000  0.000  0.000  0.000   0.3818100648\n",
      "  17  0.057  0.382  0.000  0.000  0.000  0.000   0.3793172142\n",
      "  18  0.057  0.228  0.000  0.000  0.000  0.000   0.3773378920\n",
      "  20  0.057  0.227  0.000  0.000  0.000  0.000   0.3773284999\n",
      "  32  0.057  0.227 -0.219  0.000  0.000  0.000   0.3736086435\n",
      "  33  0.057  0.227 -0.229  0.000  0.000  0.000   0.3736058011\n",
      "  34  0.057  0.227 -0.226  0.000  0.000  0.000   0.3736051409\n",
      "  35  0.057  0.227 -0.225  0.000  0.000  0.000   0.3736050531\n",
      "  44  0.057  0.227 -0.225  0.006  0.000  0.000   0.3735952782\n",
      "  58  0.057  0.227 -0.225  0.006  0.129  0.000   0.3724083627\n",
      "  60  0.057  0.227 -0.225  0.006  0.140  0.000   0.3724051561\n",
      "  62  0.057  0.227 -0.225  0.006  0.136  0.000   0.3724044375\n",
      "  63  0.057  0.227 -0.225  0.006  0.137  0.000   0.3724042810\n",
      "  71  0.057  0.227 -0.225  0.006  0.137  0.143   0.3716134257\n",
      "  73  0.057  0.227 -0.225  0.006  0.137  0.133   0.3716114907\n",
      "  77  0.057  0.227 -0.225  0.006  0.137  0.134   0.3716098064\n",
      "  powell nthiter 1: fret = 0.371610\n",
      "  86  0.166  0.227 -0.225  0.006  0.137  0.134   0.3707313187\n",
      "  87  0.168  0.227 -0.225  0.006  0.137  0.134   0.3707297246\n",
      "  88  0.173  0.227 -0.225  0.006  0.137  0.134   0.3707282421\n",
      " 108  0.173  0.227 -0.214  0.006  0.137  0.134   0.3707240851\n",
      " 110  0.173  0.227 -0.218  0.006  0.137  0.134   0.3707225847\n",
      " 119  0.173  0.227 -0.218  0.001  0.137  0.134   0.3707169683\n",
      " 121  0.173  0.227 -0.218  0.000  0.137  0.134   0.3707147566\n",
      " 122  0.173  0.227 -0.218 -0.001  0.137  0.134   0.3707146896\n",
      " 130  0.173  0.227 -0.218 -0.001  0.171  0.134   0.3707043786\n",
      " 131  0.173  0.227 -0.218 -0.001  0.156  0.134   0.3706853016\n",
      " 132  0.173  0.227 -0.218 -0.001  0.155  0.134   0.3706851790\n",
      " 140  0.173  0.227 -0.218 -0.001  0.155  0.195   0.3705246227\n",
      " 142  0.173  0.227 -0.218 -0.001  0.155  0.196   0.3705245977\n",
      " 143  0.173  0.227 -0.218 -0.001  0.155  0.197   0.3705224712\n",
      " 150  0.217  0.227 -0.215 -0.004  0.162  0.221   0.3704856626\n",
      " 151  0.203  0.227 -0.216 -0.003  0.160  0.213   0.3704704037\n",
      " 153  0.208  0.227 -0.215 -0.003  0.161  0.215   0.3704697470\n",
      " 154  0.212  0.227 -0.215 -0.003  0.161  0.217   0.3704687544\n",
      " 158  0.211  0.227 -0.215 -0.003  0.161  0.217   0.3704686964\n",
      " 159  0.211  0.227 -0.215 -0.003  0.161  0.217   0.3704684719\n",
      " 160  0.211  0.227 -0.215 -0.003  0.161  0.217   0.3704684431\n",
      " 161  0.210  0.227 -0.215 -0.003  0.161  0.217   0.3704683320\n",
      " 162  0.210  0.227 -0.215 -0.003  0.161  0.217   0.3704683094\n",
      "  powell nthiter 2: fret = 0.370468\n",
      " 181  0.210  0.229 -0.215 -0.003  0.161  0.217   0.3704613925\n",
      " 191  0.210  0.229 -0.208 -0.003  0.161  0.217   0.3704574241\n",
      " 211  0.210  0.229 -0.208 -0.003  0.184  0.217   0.3704311590\n",
      " 212  0.210  0.229 -0.208 -0.003  0.180  0.217   0.3704300135\n",
      " 214  0.210  0.229 -0.208 -0.003  0.181  0.217   0.3704299982\n",
      " 224  0.213  0.229 -0.208 -0.003  0.182  0.218   0.3704288675\n",
      " 227  0.213  0.229 -0.208 -0.003  0.182  0.218   0.3704286055\n",
      " 229  0.213  0.229 -0.208 -0.003  0.182  0.218   0.3704285782\n",
      "  powell nthiter 3: fret = 0.370429\n",
      " 240  0.213  0.229 -0.208 -0.003  0.182  0.222   0.3704245179\n",
      " 242  0.213  0.229 -0.208 -0.003  0.182  0.221   0.3704227043\n",
      " 264  0.213  0.229 -0.207 -0.003  0.182  0.221   0.3704226941\n",
      " 297  0.213  0.229 -0.207 -0.003  0.182  0.221   0.3704225904\n",
      " 299  0.212  0.229 -0.207 -0.003  0.181  0.220   0.3704221772\n",
      " 303  0.212  0.229 -0.207 -0.003  0.182  0.220   0.3704221503\n",
      " 310  0.212  0.229 -0.207 -0.003  0.181  0.221   0.3704216514\n",
      " 312  0.212  0.229 -0.207 -0.003  0.181  0.221   0.3704216473\n",
      " 313  0.212  0.229 -0.207 -0.003  0.181  0.221   0.3704216454\n",
      " 315  0.212  0.229 -0.207 -0.003  0.181  0.221   0.3704216308\n",
      " 318  0.212  0.229 -0.207 -0.003  0.181  0.221   0.3704216179\n",
      " 319  0.212  0.229 -0.207 -0.003  0.181  0.221   0.3704216141\n",
      "  powell nthiter 4: fret = 0.370422\n",
      " 329  0.211  0.229 -0.207 -0.003  0.181  0.221   0.3704214335\n",
      " 331  0.211  0.229 -0.207 -0.003  0.181  0.221   0.3704214096\n",
      " 332  0.211  0.229 -0.207 -0.003  0.181  0.221   0.3704212331\n",
      " 382  0.210  0.229 -0.206 -0.003  0.181  0.221   0.3704208267\n",
      " 387  0.210  0.229 -0.206 -0.003  0.181  0.221   0.3704208162\n",
      "  powell nthiter 5: fret = 0.370421\n",
      " 403  0.210  0.229 -0.206 -0.003  0.181  0.221   0.3704206774\n",
      " 404  0.210  0.229 -0.206 -0.003  0.181  0.221   0.3704206749\n",
      " 426  0.210  0.229 -0.207 -0.003  0.181  0.221   0.3704206312\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " 452  0.209  0.229 -0.207 -0.003  0.181  0.222   0.3704203080\n",
      " 458  0.209  0.229 -0.207 -0.003  0.181  0.222   0.3704203076\n",
      " 460  0.209  0.229 -0.207 -0.003  0.181  0.222   0.3704202882\n",
      " 463  0.208  0.229 -0.208 -0.003  0.181  0.222   0.3704202378\n",
      " 469  0.209  0.229 -0.208 -0.003  0.181  0.222   0.3704202128\n",
      " 475  0.209  0.229 -0.208 -0.003  0.181  0.222   0.3704201737\n",
      " 477  0.209  0.229 -0.208 -0.003  0.181  0.222   0.3704201709\n",
      " 480  0.209  0.229 -0.208 -0.003  0.181  0.222   0.3704201589\n",
      " 481  0.209  0.229 -0.208 -0.003  0.181  0.222   0.3704201552\n",
      "  powell nthiter 6: fret = 0.370420\n",
      " 549  0.209  0.229 -0.208 -0.003  0.181  0.222   0.3704201471\n",
      "Powell done niters = 6\n",
      "Computing relative cost\n",
      " 0  -25.0 -25.0 -25.0   1.010189\n",
      " 1  -25.0 -25.0  25.0   1.015533\n",
      " 2  -25.0  25.0 -25.0   1.036327\n",
      " 3  -25.0  25.0  25.0   1.020098\n",
      " 4   25.0 -25.0 -25.0   1.016792\n",
      " 5   25.0 -25.0  25.0   1.035460\n",
      " 6   25.0  25.0 -25.0   1.039669\n",
      " 7   25.0  25.0  25.0   1.021760\n",
      "REL:  8  0.370420    8.195828  1.024479 rel = 0.361569 \n",
      "Number of iterations     6\n",
      "Min cost was 0.370420\n",
      "Number of FunctionCalls   553\n",
      "TolPowell 0.000000\n",
      "nMaxItersPowell 36\n",
      "OptimizationTime 21.831000 sec\n",
      "Parameters at optimum (transmm)  0.20869  0.22910 -0.20754\n",
      "Parameters at optimum (rotdeg) -0.00301  0.18099  0.22192 \n",
      "Final costs ----------------\n",
      "Number of surface hits 164751\n",
      "WM  Intensity   744.1257 +/- 118.5461\n",
      "Ctx Intensity   826.4495 +/- 168.1570\n",
      "Pct Contrast      8.9186 +/-  21.9576\n",
      "Cost   0.3704\n",
      "RelCost   0.3730\n",
      "Reg at min cost was \n",
      " 0.99914   0.04092  -0.00700   1.31835;\n",
      " 0.01696  -0.24865   0.96845  -20.82578;\n",
      "-0.03789   0.96773   0.24913   6.02415;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Writing optimal reg to bold/register.dof6.dat, type = 14 \n",
      "Original Reg \n",
      " 0.99931   0.03690  -0.00403   1.00841;\n",
      " 0.01310  -0.24886   0.96845  -21.05935;\n",
      "-0.03473   0.96784   0.24917   6.23380;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Original Reg - Optimal Reg\n",
      " 0.00017  -0.00402   0.00296  -0.30994;\n",
      "-0.00387  -0.00021   0.00001  -0.23357;\n",
      " 0.00316   0.00011   0.00004   0.20965;\n",
      " 0.00000   0.00000   0.00000   0.00000;\n",
      "\n",
      "Computing change in lh position\n",
      "LH rmsDiffMean 0.252217\n",
      "Computing change in rh position\n",
      "Surface-RMS-Diff-mm 0.362554 0.141031 0.652399\n",
      "mri_segreg done\n",
      "MinCost: 0.370420 744.125688 826.449488 8.918626 \n",
      "tkregister2_cmdl --mov bold/template.nii.gz --reg bold/register.dof6.dat --noedit --ltaout bold/register.dof6.lta\n",
      "tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl\n",
      "INFO: no target volume specified, assuming FreeSurfer orig volume.\n",
      "target  volume orig\n",
      "movable volume bold/template.nii.gz\n",
      "reg file       bold/register.dof6.dat\n",
      "LoadVol        0\n",
      "ZeroCRAS       0\n",
      "$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $\n",
      "Diagnostic Level -1\n",
      "---- Input registration matrix --------\n",
      " 0.99914   0.04092  -0.00700   1.31835;\n",
      " 0.01696  -0.24865   0.96845  -20.82578;\n",
      "-0.03789   0.96773   0.24913   6.02415;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "float2int = 0\n",
      "---------------------------------------\n",
      "INFO: loading target /usr/local/freesurfer/subjects/pBrain/mri/orig.mgz\n",
      "Ttarg: --------------------\n",
      "-1.00000   0.00000   0.00000   128.00000;\n",
      " 0.00000   0.00000   1.00000  -128.00000;\n",
      " 0.00000  -1.00000   0.00000   128.00000;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "INFO: loading movable bold/template.nii.gz\n",
      "Tmov: --------------------\n",
      "-2.00000   0.00000   0.00000   128.00000;\n",
      " 0.00000   0.00000   2.00000  -40.00000;\n",
      " 0.00000  -2.00000   0.00000   128.00000;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "mkheaderreg = 0, float2int = 0\n",
      "---- Input registration matrix --------\n",
      " 0.99914   0.04092  -0.00700   1.31835;\n",
      " 0.01696  -0.24865   0.96845  -20.82578;\n",
      "-0.03789   0.96773   0.24913   6.02415;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Determinant -1\n",
      "subject = pBrain\n",
      "RegMat ---------------------------\n",
      " 0.99914   0.04092  -0.00700   1.31835;\n",
      " 0.01696  -0.24865   0.96845  -20.82578;\n",
      "-0.03789   0.96773   0.24913   6.02415;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Cleaning up\n",
      " \n",
      "Started at Fri Nov 24 12:59:45 CET 2017 \n",
      "Ended   at Fri Nov 24 13:01:02 CET 2017\n",
      "BBR-Run-Time-Sec 77\n",
      " \n",
      "bbregister Done\n",
      "To check results, run:\n",
      "tkregisterfv --mov bold/template.nii.gz --reg bold/register.dof6.lta --surfs \n",
      " \n",
      "  Run: 003 ----------------\n",
      "Fri Nov 24 13:01:03 CET 2017\n",
      "--------------------------------------\n",
      "/data/martin/prosopagnosia/landscapes/Sess01\n",
      "bbregister --s pBrain --init-coreg --6 --bold --mov bold/003/template.nii.gz --reg bold/003/register.dof6.dat --lta bold/003/register.dof6.lta --init-reg-out bold/003/init.register.dof6.dat\n",
      "tmp bold/003/tmp.bbregister.22954\n",
      "Log file is bold/003/register.dof6.dat.log\n",
      "Fri Nov 24 13:01:03 CET 2017\n",
      "\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/landscapes/Sess01\n",
      "/usr/local/freesurfer/bin/bbregister --s pBrain --init-coreg --6 --bold --mov bold/003/template.nii.gz --reg bold/003/register.dof6.dat --lta bold/003/register.dof6.lta --init-reg-out bold/003/init.register.dof6.dat\n",
      "\n",
      "$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "FREESURFER_HOME /usr/local/freesurfer\n",
      "mri_convert bold/003/template.nii.gz bold/003/tmp.bbregister.22954/template.nii\n",
      "mri_convert.bin bold/003/template.nii.gz bold/003/tmp.bbregister.22954/template.nii \n",
      "$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $\n",
      "reading from bold/003/template.nii.gz...\n",
      "TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00\n",
      "i_ras = (-0.999463, -0.0273032, 0.0181267)\n",
      "j_ras = (0.022681, -0.975511, -0.21878)\n",
      "k_ras = (0.0236561, -0.218251, 0.975606)\n",
      "writing to bold/003/tmp.bbregister.22954/template.nii...\n",
      "mri_coreg --s pBrain --mov bold/003/tmp.bbregister.22954/template.nii --regdat bold/003/tmp.bbregister.22954/reg.init.dat --reg bold/003/tmp.bbregister.22954/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01\n",
      "\n",
      "$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/landscapes/Sess01\n",
      "cmdline mri_coreg --s pBrain --mov bold/003/tmp.bbregister.22954/template.nii --regdat bold/003/tmp.bbregister.22954/reg.init.dat --reg bold/003/tmp.bbregister.22954/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "dof    6\n",
      "nsep    1\n",
      "cras0    1\n",
      "ftol    0.000100\n",
      "linmintol    0.010000\n",
      "bf       1\n",
      "bflim    30.000000\n",
      "bfnsamp    30\n",
      "SmoothRef 0\n",
      "SatPct    99.990000\n",
      "MovOOB 0\n",
      "optschema 1\n",
      "Reading in mov bold/003/tmp.bbregister.22954/template.nii\n",
      "Reading in ref /usr/local/freesurfer/subjects/pBrain/mri/brainmask.mgz\n",
      "Reading in and applying refmask /usr/local/freesurfer/subjects/pBrain/mri/aparc+aseg.mgz\n",
      "Setting cras translation parameters to align centers\n",
      "Creating random numbers for coordinate dithering\n",
      "Performing intensity dithering\n",
      "Initial parameters  4.8266 -14.2690  7.8386  0.0000  0.0000  0.0000  1.0000  1.0000  1.0000  0.0000  0.0000  0.0000 \n",
      "Separation list (1):  4   min = 4\n",
      "DoSmoothing 1\n",
      "DoCoordDither 1\n",
      "DoIntensityDither 1\n",
      "nitersmax 4\n",
      "ftol 1.000e-04\n",
      "linmintol 1.000e-02\n",
      "SatPct 99.990000\n",
      "Hist FWHM 7.000000 7.000000\n",
      "nthreads 1\n",
      "movsat = 1676.6666\n",
      "mov gstd 1.6917 1.6917 1.6917\n",
      "Smoothing mov\n",
      "refsat = 115.0000\n",
      "ref gstd 1.8914 1.8914 1.8914\n",
      "Smoothing ref\n",
      "COREGpreproc() done\n",
      "Testing if mov and target overlap\n",
      "Init cost   -1.0419996173\n",
      "nhits = 78038 out of 16777216, Percent Overlap:  29.8\n",
      "Initial  RefRAS-to-MovRAS\n",
      " 1.00000   0.00000   0.00000   4.82664;\n",
      " 0.00000   1.00000   0.00000  -14.26899;\n",
      " 0.00000   0.00000   1.00000   7.83862;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Initial  RefVox-to-MovVox\n",
      " 0.49973  -0.00906  -0.01365   2.68039;\n",
      "-0.01134   0.10939  -0.48776   113.18749;\n",
      "-0.01183  -0.48780  -0.10913   97.11647;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "sep = 4 -----------------------------------\n",
      "COREGoptBruteForce() 30 1 30\n",
      "Turning on MovOOB for BruteForce Search\n",
      "#BF# sep= 4 iter=0 lim=30.0 delta=2.00   4.82664  -0.26899 -10.16138   2.00000   2.00000   2.00000   -1.0316520\n",
      "Turning  MovOOB back off after brute force search\n",
      "\n",
      "\n",
      "---------------------------------\n",
      "Init Powel Params dof = 6\n",
      "Starting OpenPowel2(), sep = 4\n",
      "InitialCost        -1.0705379248 \n",
      "#@#  4  188  4.82664 -0.26899 -10.16138 2.00000 2.00000 2.00000   -1.0705379\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "fs_powell::minimize\n",
      "  nparams 6\n",
      "  maxfev 4\n",
      "  ftol   0.000100\n",
      "  linmin_xtol_   0.010000\n",
      "  powell nthiter 0: fret = -1.070538\n",
      "#@#  4  190  5.82664 -0.26899 -10.16138 2.00000 2.00000 2.00000   -1.0707175\n",
      "#@#  4  194  5.44467 -0.26899 -10.16138 2.00000 2.00000 2.00000   -1.0707406\n",
      "#@#  4  195  5.53955 -0.26899 -10.16138 2.00000 2.00000 2.00000   -1.0707440\n",
      "#@#  4  196  5.54955 -0.26899 -10.16138 2.00000 2.00000 2.00000   -1.0707448\n",
      "#@#  4  202  5.54955 -1.88702 -10.16138 2.00000 2.00000 2.00000   -1.0726600\n",
      "#@#  4  205  5.54955 -3.38949 -10.16138 2.00000 2.00000 2.00000   -1.0733769\n",
      "#@#  4  208  5.54955 -3.36901 -10.16138 2.00000 2.00000 2.00000   -1.0733807\n",
      "#@#  4  209  5.54955 -3.37901 -10.16138 2.00000 2.00000 2.00000   -1.0733827\n",
      "#@#  4  211  5.54955 -3.37901 -9.16138 2.00000 2.00000 2.00000   -1.0741190\n",
      "#@#  4  214  5.54955 -3.37901 -8.54335 2.00000 2.00000 2.00000   -1.0742674\n",
      "#@#  4  216  5.54955 -3.37901 -8.55400 2.00000 2.00000 2.00000   -1.0742675\n",
      "#@#  4  220  5.54955 -3.37901 -8.55400 0.38197 2.00000 2.00000   -1.0746046\n",
      "#@#  4  221  5.54955 -3.37901 -8.55400 0.76030 2.00000 2.00000   -1.0746506\n",
      "#@#  4  228  5.54955 -3.37901 -8.55400 0.79503 2.00000 2.00000   -1.0746517\n",
      "#@#  4  229  5.54955 -3.37901 -8.55400 0.80650 2.00000 2.00000   -1.0746536\n",
      "#@#  4  232  5.54955 -3.37901 -8.55400 0.80650 0.38197 2.00000   -1.0749613\n",
      "#@#  4  233  5.54955 -3.37901 -8.55400 0.80650 0.57282 2.00000   -1.0749781\n",
      "#@#  4  237  5.54955 -3.37901 -8.55400 0.80650 0.65235 2.00000   -1.0749800\n",
      "#@#  4  238  5.54955 -3.37901 -8.55400 0.80650 0.62716 2.00000   -1.0749810\n",
      "#@#  4  240  5.54955 -3.37901 -8.55400 0.80650 0.63716 2.00000   -1.0749831\n",
      "#@#  4  245  5.54955 -3.37901 -8.55400 0.80650 0.63716 1.38197   -1.0750204\n",
      "#@#  4  247  5.54955 -3.37901 -8.55400 0.80650 0.63716 1.62974   -1.0750568\n",
      "#@#  4  249  5.54955 -3.37901 -8.55400 0.80650 0.63716 1.61673   -1.0750571\n",
      "  powell nthiter 1: fret = -1.075057\n",
      "#@#  4  269  5.54955 -3.47200 -8.55400 0.80650 0.63716 1.61673   -1.0750645\n",
      "#@#  4  270  5.54955 -3.53975 -8.55400 0.80650 0.63716 1.61673   -1.0750654\n",
      "#@#  4  275  5.54955 -3.54975 -8.55400 0.80650 0.63716 1.61673   -1.0750663\n",
      "#@#  4  281  5.54955 -3.54975 -8.17204 0.80650 0.63716 1.61673   -1.0751157\n",
      "#@#  4  282  5.54955 -3.54975 -8.23059 0.80650 0.63716 1.61673   -1.0751202\n",
      "#@#  4  283  5.54955 -3.54975 -8.26187 0.80650 0.63716 1.61673   -1.0751286\n",
      "#@#  4  294  5.54955 -3.54975 -8.26187 0.57867 0.63716 1.61673   -1.0751458\n",
      "#@#  4  295  5.54955 -3.54975 -8.26187 0.59297 0.63716 1.61673   -1.0751506\n",
      "#@#  4  309  5.54955 -3.54975 -8.26187 0.59297 0.62716 1.61673   -1.0751508\n",
      "Powell done niters total = 1\n",
      "OptTimeSec  5.2 sec\n",
      "OptTimeMin  0.09 min\n",
      "nEvals 321\n",
      "Final parameters   5.54954910  -3.54975486  -8.26187420   0.59296590   0.62716258   1.61673009 \n",
      "Final cost   -1.075150842973271\n",
      " \n",
      "\n",
      "---------------------------------\n",
      "mri_coreg utimesec    43.528000\n",
      "mri_coreg stimesec    0.084000\n",
      "mri_coreg ru_maxrss   426972\n",
      "mri_coreg ru_ixrss    0\n",
      "mri_coreg ru_idrss    0\n",
      "mri_coreg ru_isrss    0\n",
      "mri_coreg ru_minflt   126903\n",
      "mri_coreg ru_majflt   0\n",
      "mri_coreg ru_nswap    0\n",
      "mri_coreg ru_inblock  0\n",
      "mri_coreg ru_oublock  0\n",
      "mri_coreg ru_msgsnd   0\n",
      "mri_coreg ru_msgrcv   0\n",
      "mri_coreg ru_nsignals 0\n",
      "mri_coreg ru_nvcsw    47\n",
      "mri_coreg ru_nivcsw   111\n",
      "Final  RefRAS-to-MovRAS\n",
      " 0.99954   0.02821   0.01095   5.54955;\n",
      "-0.02833   0.99955   0.01035  -3.54975;\n",
      "-0.01065  -0.01065   0.99989  -8.26187;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Final  RefVox-to-MovVox\n",
      " 0.49921  -0.00345  -0.02784   3.30041;\n",
      "-0.02632   0.11430  -0.48605   110.88343;\n",
      "-0.00972  -0.48675  -0.11394   88.33469;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Final parameters  5.5495 -3.5498 -8.2619  0.5930  0.6272  1.6167 \n",
      "nhits = 75683 out of 16777216, Percent Overlap:  28.9\n",
      "mri_coreg RunTimeSec 43.6 sec\n",
      "To check run:\n",
      "   tkregisterfv --mov bold/003/tmp.bbregister.22954/template.nii --targ /usr/local/freesurfer/subjects/pBrain/mri/brainmask.mgz --reg bold/003/tmp.bbregister.22954/mri_coreg.lta --s pBrain --surfs \n",
      "\n",
      "mri_coreg done\n",
      "\n",
      "mri_segreg --mov bold/003/tmp.bbregister.22954/template.nii --init-reg bold/003/tmp.bbregister.22954/reg.init.dat --out-reg bold/003/tmp.bbregister.22954/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5\n",
      "$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/landscapes/Sess01\n",
      "mri_segreg --mov bold/003/tmp.bbregister.22954/template.nii --init-reg bold/003/tmp.bbregister.22954/reg.init.dat --out-reg bold/003/tmp.bbregister.22954/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "movvol bold/003/tmp.bbregister.22954/template.nii\n",
      "regfile bold/003/tmp.bbregister.22954/reg.init.dat\n",
      "subject pBrain\n",
      "dof 6\n",
      "outregfile bold/003/tmp.bbregister.22954/bbr.pass1.dat\n",
      "UseMask 0\n",
      "UseLH 1\n",
      "UseRH 1\n",
      "nsubsamp 100\n",
      "PenaltySign  -1\n",
      "PenaltySlope 0.500000\n",
      "PenaltyCenter 0.000000\n",
      "surfname white\n",
      "GMProjFrac 0.500000\n",
      "WMProjAbs 2.000000\n",
      "lhcostfile (null)\n",
      "rhcostfile (null)\n",
      "interp  trilinear (1)\n",
      "frame  0\n",
      "TolPowell 0.000100\n",
      "nMaxItersPowell 36\n",
      "n1dmin  3\n",
      "Profile   0\n",
      "Gdiag_no  -1\n",
      "AddNoise  0 (0)\n",
      "SynthSeed 1512293037\n",
      "TransRandMax 0.000000\n",
      "RotRandMax 0.000000\n",
      "Translations 0.000000 0.000000 0.000000\n",
      "Rotations   0.000000 0.000000 0.000000\n",
      "Input reg\n",
      " 0.99842   0.05568  -0.00690   1.61143;\n",
      " 0.01944  -0.22788   0.97350  -19.59457;\n",
      "-0.05263   0.97210   0.22860   8.13734;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Loading mov\n",
      "Projecting LH Surfs\n",
      "Loading lh.white surf\n",
      "Loading lh.thickness for GM\n",
      "GM Proj: 1 0.500000 2.000000\n",
      "WM Proj: 0 0.500000 2.000000\n",
      "Projecting RH Surfs\n",
      "Loading rh.white surf\n",
      "Loading rh.thickness for GM\n",
      "Projecting RH Surfs\n",
      "Using lh.cortex.label\n",
      "Using rh.cortex.label\n",
      "Computing relative cost\n",
      " 0  -25.0 -25.0 -25.0   0.986424\n",
      " 1  -25.0 -25.0  25.0   1.050263\n",
      " 2  -25.0  25.0 -25.0   1.034481\n",
      " 3  -25.0  25.0  25.0   0.989399\n",
      " 4   25.0 -25.0 -25.0   1.022769\n",
      " 5   25.0 -25.0  25.0   1.081380\n",
      " 6   25.0  25.0 -25.0   1.076422\n",
      " 7   25.0  25.0  25.0   1.026991\n",
      "REL:  8  0.564896    8.268130  1.033516 rel = 0.546577 \n",
      "Initial costs ----------------\n",
      "Number of surface hits 1618\n",
      "WM  Intensity   767.5330 +/- 106.2986\n",
      "Ctx Intensity   821.3665 +/- 156.3536\n",
      "Pct Contrast      5.2494 +/-  21.4901\n",
      "Cost   0.5649\n",
      "RelCost   0.5466\n",
      "\n",
      "------------------------------------\n",
      "Brute force preopt -4 4 4, n = 729\n",
      "     0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      1.0901   1.0901  0.0\n",
      "     1  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   0.0000      1.0828   1.0828  0.0\n",
      "     2  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   4.0000      1.0706   1.0706  0.0\n",
      "     3  -4.0000  -4.0000  -4.0000  -4.0000   0.0000  -4.0000      1.0177   1.0177  0.0\n",
      "     6  -4.0000  -4.0000  -4.0000  -4.0000   4.0000  -4.0000      0.9436   0.9436  0.0\n",
      "    15  -4.0000  -4.0000  -4.0000   0.0000   4.0000  -4.0000      0.9382   0.9382  0.0\n",
      "    45  -4.0000  -4.0000   0.0000   4.0000  -4.0000  -4.0000      0.8844   0.8844  0.0\n",
      "   117  -4.0000   0.0000   0.0000   0.0000  -4.0000  -4.0000      0.8538   0.8538  0.0\n",
      "   118  -4.0000   0.0000   0.0000   0.0000  -4.0000   0.0000      0.8352   0.8352  0.0\n",
      "   292   0.0000  -4.0000   0.0000   4.0000   0.0000   0.0000      0.7735   0.7735  0.0\n",
      "   337   0.0000   0.0000  -4.0000   0.0000   0.0000   0.0000      0.7309   0.7309  0.0\n",
      "   346   0.0000   0.0000  -4.0000   4.0000   0.0000   0.0000      0.6993   0.6993  0.0\n",
      "   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.5649   0.5649  0.0\n",
      "Brute Force --------------------------\n",
      "Min cost was 0.564896\n",
      "Number of iterations   729\n",
      "Search time 0.627000 sec\n",
      "Parameters at best (transmm, rotdeg)\n",
      "  0.000   0.000   0.000  0.000  0.000  0.000 \n",
      "--------------------------------------------\n",
      "\n",
      "Starting Powell Minimization\n",
      "Init Powel Params dof = 6\n",
      "0 0\n",
      "1 0\n",
      "2 0\n",
      "3 0\n",
      "4 0\n",
      "5 0\n",
      "fs_powell::minimize\n",
      "  nparams 6\n",
      "  maxfev 36\n",
      "  ftol   0.000100\n",
      "  linmin_xtol_   0.001000\n",
      "  powell nthiter 0: fret = 0.564896\n",
      "   6  0.382  0.000  0.000  0.000  0.000  0.000   0.5633483167\n",
      "   7  0.245  0.000  0.000  0.000  0.000  0.000   0.5619856765\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "   9  0.270  0.000  0.000  0.000  0.000  0.000   0.5619079717\n",
      "  16  0.270 -0.618  0.000  0.000  0.000  0.000   0.5398575285\n",
      "  18  0.270 -0.592  0.000  0.000  0.000  0.000   0.5394087308\n",
      "  21  0.270 -0.562  0.000  0.000  0.000  0.000   0.5392840695\n",
      "  25  0.270 -0.559  0.000  0.000  0.000  0.000   0.5392448097\n",
      "  30  0.270 -0.559 -1.618  0.000  0.000  0.000   0.4988232690\n",
      "  31  0.270 -0.559 -1.169  0.000  0.000  0.000   0.4987252778\n",
      "  33  0.270 -0.559 -0.722  0.000  0.000  0.000   0.4964495583\n",
      "  35  0.270 -0.559 -0.905  0.000  0.000  0.000   0.4948376714\n",
      "  36  0.270 -0.559 -0.897  0.000  0.000  0.000   0.4947393795\n",
      "  37  0.270 -0.559 -0.848  0.000  0.000  0.000   0.4946303726\n",
      "  39  0.270 -0.559 -0.867  0.000  0.000  0.000   0.4946005238\n",
      "  40  0.270 -0.559 -0.864  0.000  0.000  0.000   0.4945996366\n",
      "  41  0.270 -0.559 -0.865  0.000  0.000  0.000   0.4945995427\n",
      "  44  0.270 -0.559 -0.865  1.000  0.000  0.000   0.4696144395\n",
      "  48  0.270 -0.559 -0.865  0.618  0.000  0.000   0.4585986454\n",
      "  50  0.270 -0.559 -0.865  0.647  0.000  0.000   0.4585745920\n",
      "  51  0.270 -0.559 -0.865  0.637  0.000  0.000   0.4585630154\n",
      "  52  0.270 -0.559 -0.865  0.636  0.000  0.000   0.4585629619\n",
      "  58  0.270 -0.559 -0.865  0.636 -0.618  0.000   0.4392791996\n",
      "  63  0.270 -0.559 -0.865  0.636 -0.607  0.000   0.4392380932\n",
      "  64  0.270 -0.559 -0.865  0.636 -0.605  0.000   0.4392361208\n",
      "  75  0.270 -0.559 -0.865  0.636 -0.605  0.021   0.4392184367\n",
      "  powell nthiter 1: fret = 0.439218\n",
      "  88 -0.348 -0.559 -0.865  0.636 -0.605  0.022   0.4195272978\n",
      "  90 -0.195 -0.559 -0.865  0.636 -0.605  0.022   0.4186596333\n",
      "  91 -0.236 -0.559 -0.865  0.636 -0.605  0.022   0.4179703420\n",
      "  92 -0.257 -0.559 -0.865  0.636 -0.605  0.022   0.4178390669\n",
      "  93 -0.265 -0.559 -0.865  0.636 -0.605  0.022   0.4178132114\n",
      "  96 -0.270 -0.559 -0.865  0.636 -0.605  0.022   0.4178073902\n",
      " 105 -0.270 -0.816 -0.865  0.636 -0.605  0.022   0.4162037252\n",
      " 108 -0.270 -0.867 -0.865  0.636 -0.605  0.022   0.4161438755\n",
      " 109 -0.270 -0.858 -0.865  0.636 -0.605  0.022   0.4160636967\n",
      " 110 -0.270 -0.844 -0.865  0.636 -0.605  0.022   0.4159618714\n",
      " 113 -0.270 -0.840 -0.865  0.636 -0.605  0.022   0.4159285496\n",
      " 116 -0.270 -0.839 -0.865  0.636 -0.605  0.022   0.4159195662\n",
      " 123 -0.270 -0.839 -1.165  0.636 -0.605  0.022   0.4149630135\n",
      " 126 -0.270 -0.839 -1.150  0.636 -0.605  0.022   0.4149621463\n",
      " 127 -0.270 -0.839 -1.157  0.636 -0.605  0.022   0.4149558660\n",
      " 128 -0.270 -0.839 -1.158  0.636 -0.605  0.022   0.4149558478\n",
      " 131 -0.270 -0.839 -1.158  1.636 -0.605  0.022   0.4091666772\n",
      " 135 -0.270 -0.839 -1.158  1.254 -0.605  0.022   0.3928333719\n",
      " 136 -0.270 -0.839 -1.158  1.140 -0.605  0.022   0.3904262966\n",
      " 138 -0.270 -0.839 -1.158  1.115 -0.605  0.022   0.3901337320\n",
      " 140 -0.270 -0.839 -1.158  1.086 -0.605  0.022   0.3896421698\n",
      " 142 -0.270 -0.839 -1.158  1.089 -0.605  0.022   0.3896308439\n",
      " 145 -0.270 -0.839 -1.158  1.090 -0.605  0.022   0.3896274292\n",
      " 152 -0.270 -0.839 -1.158  1.090 -0.809  0.022   0.3842492244\n",
      " 154 -0.270 -0.839 -1.158  1.090 -0.780  0.022   0.3840057027\n",
      " 157 -0.270 -0.839 -1.158  1.090 -0.772  0.022   0.3839862395\n",
      " 159 -0.270 -0.839 -1.158  1.090 -0.773  0.022   0.3839849650\n",
      " 161 -0.270 -0.839 -1.158  1.090 -0.774  0.022   0.3839840802\n",
      " 166 -0.270 -0.839 -1.158  1.090 -0.774 -0.596   0.3797641664\n",
      " 168 -0.270 -0.839 -1.158  1.090 -0.774 -0.439   0.3782032069\n",
      " 169 -0.270 -0.839 -1.158  1.090 -0.774 -0.381   0.3776650087\n",
      " 170 -0.270 -0.839 -1.158  1.090 -0.774 -0.227   0.3768577136\n",
      " 172 -0.270 -0.839 -1.158  1.090 -0.774 -0.278   0.3765417934\n",
      " 174 -0.270 -0.839 -1.158  1.090 -0.774 -0.273   0.3765354653\n",
      " 176 -0.270 -0.839 -1.158  1.090 -0.774 -0.271   0.3765352684\n",
      "  powell nthiter 2: fret = 0.376535\n",
      " 186 -0.305 -0.839 -1.158  1.090 -0.774 -0.271   0.3754846110\n",
      " 188 -0.384 -0.839 -1.158  1.090 -0.774 -0.271   0.3749915843\n",
      " 189 -0.360 -0.839 -1.158  1.090 -0.774 -0.271   0.3748410861\n",
      " 199 -0.360 -0.855 -1.158  1.090 -0.774 -0.271   0.3746786229\n",
      " 200 -0.360 -0.890 -1.158  1.090 -0.774 -0.271   0.3738950366\n",
      " 203 -0.360 -0.877 -1.158  1.090 -0.774 -0.271   0.3737683857\n",
      " 206 -0.360 -0.874 -1.158  1.090 -0.774 -0.271   0.3737511635\n",
      " 207 -0.360 -0.872 -1.158  1.090 -0.774 -0.271   0.3737433029\n",
      " 208 -0.360 -0.871 -1.158  1.090 -0.774 -0.271   0.3737403582\n",
      " 216 -0.360 -0.871 -1.223  1.090 -0.774 -0.271   0.3732733550\n",
      " 218 -0.360 -0.871 -1.222  1.090 -0.774 -0.271   0.3732730941\n",
      " 239 -0.360 -0.871 -1.222  1.090 -0.854 -0.271   0.3729556557\n",
      " 240 -0.360 -0.871 -1.222  1.090 -0.832 -0.271   0.3728383708\n",
      " 241 -0.360 -0.871 -1.222  1.090 -0.826 -0.271   0.3728234707\n",
      " 243 -0.360 -0.871 -1.222  1.090 -0.822 -0.271   0.3728167100\n",
      " 244 -0.360 -0.871 -1.222  1.090 -0.817 -0.271   0.3728148876\n",
      " 245 -0.360 -0.871 -1.222  1.090 -0.818 -0.271   0.3728142015\n",
      " 260 -0.360 -0.871 -1.222  1.090 -0.818 -0.272   0.3728105988\n",
      "  powell nthiter 3: fret = 0.372811\n",
      " 271 -0.419 -0.871 -1.222  1.090 -0.818 -0.272   0.3726043301\n",
      " 272 -0.398 -0.871 -1.222  1.090 -0.818 -0.272   0.3725375245\n",
      " 273 -0.400 -0.871 -1.222  1.090 -0.818 -0.272   0.3725374415\n",
      " 285 -0.400 -0.874 -1.222  1.090 -0.818 -0.272   0.3725340035\n",
      " 313 -0.400 -0.874 -1.222  1.093 -0.818 -0.272   0.3725282416\n",
      " 314 -0.400 -0.874 -1.222  1.094 -0.818 -0.272   0.3725247946\n",
      " 315 -0.400 -0.874 -1.222  1.095 -0.818 -0.272   0.3725234274\n",
      " 325 -0.400 -0.874 -1.222  1.095 -0.820 -0.272   0.3725225442\n",
      " 354 -0.399 -0.874 -1.222  1.095 -0.820 -0.272   0.3725223956\n",
      "  powell nthiter 4: fret = 0.372522\n",
      " 383 -0.399 -0.876 -1.222  1.095 -0.820 -0.272   0.3725207595\n",
      " 384 -0.399 -0.877 -1.222  1.095 -0.820 -0.272   0.3725205583\n",
      " 400 -0.399 -0.877 -1.221  1.095 -0.820 -0.272   0.3725203856\n",
      " 412 -0.399 -0.877 -1.221  1.102 -0.820 -0.272   0.3725147133\n",
      " 437 -0.399 -0.877 -1.221  1.102 -0.820 -0.272   0.3725146840\n",
      "Powell done niters = 4\n",
      "Computing relative cost\n",
      " 0  -25.0 -25.0 -25.0   1.024176\n",
      " 1  -25.0 -25.0  25.0   1.007638\n",
      " 2  -25.0  25.0 -25.0   1.014709\n",
      " 3  -25.0  25.0  25.0   0.998686\n",
      " 4   25.0 -25.0 -25.0   0.995801\n",
      " 5   25.0 -25.0  25.0   1.080818\n",
      " 6   25.0  25.0 -25.0   1.071381\n",
      " 7   25.0  25.0  25.0   1.018527\n",
      "REL:  8  0.372515    8.211736  1.026467 rel = 0.36291 \n",
      "Number of iterations     4\n",
      "Min cost was 0.372515\n",
      "Number of FunctionCalls   440\n",
      "TolPowell 0.000100\n",
      "nMaxItersPowell 36\n",
      "OptimizationTime 0.400000 sec\n",
      "Parameters at optimum (transmm) -0.39916 -0.87663 -1.22114\n",
      "Parameters at optimum (rotdeg)  1.10163 -0.81986 -0.27178 \n",
      "Final costs ----------------\n",
      "Number of surface hits 1646\n",
      "WM  Intensity   746.8248 +/- 114.0761\n",
      "Ctx Intensity   826.9249 +/- 165.6577\n",
      "Pct Contrast      8.5491 +/-  22.0277\n",
      "Cost   0.3725\n",
      "RelCost   0.5466\n",
      "Reg at min cost was \n",
      " 0.99916   0.04066  -0.00584   1.00740;\n",
      " 0.01571  -0.24672   0.96896  -20.63093;\n",
      "-0.03796   0.96823   0.24715   6.56025;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Writing optimal reg to bold/003/tmp.bbregister.22954/bbr.pass1.dat, type = 14 \n",
      "Original Reg \n",
      " 0.99842   0.05568  -0.00690   1.61143;\n",
      " 0.01944  -0.22788   0.97350  -19.59457;\n",
      "-0.05263   0.97210   0.22860   8.13734;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Original Reg - Optimal Reg\n",
      "-0.00073   0.01502  -0.00106   0.60403;\n",
      " 0.00373   0.01884   0.00454   1.03635;\n",
      "-0.01468   0.00386  -0.01855   1.57710;\n",
      " 0.00000   0.00000   0.00000   0.00000;\n",
      "\n",
      "Computing change in lh position\n",
      "LH rmsDiffMean 1.602691\n",
      "Computing change in rh position\n",
      "Surface-RMS-Diff-mm 1.437977 0.592914 2.917162\n",
      "mri_segreg done\n",
      "mri_segreg --mov bold/003/tmp.bbregister.22954/template.nii --init-reg bold/003/tmp.bbregister.22954/bbr.pass1.dat --out-reg bold/003/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/003/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/003/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/003/tmp.bbregister.22954/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5\n",
      "$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/landscapes/Sess01\n",
      "mri_segreg --mov bold/003/tmp.bbregister.22954/template.nii --init-reg bold/003/tmp.bbregister.22954/bbr.pass1.dat --out-reg bold/003/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/003/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/003/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/003/tmp.bbregister.22954/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 \n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "movvol bold/003/tmp.bbregister.22954/template.nii\n",
      "regfile bold/003/tmp.bbregister.22954/bbr.pass1.dat\n",
      "subject pBrain\n",
      "dof 6\n",
      "outregfile bold/003/register.dof6.dat\n",
      "UseMask 0\n",
      "UseLH 1\n",
      "UseRH 1\n",
      "nsubsamp 1\n",
      "PenaltySign  -1\n",
      "PenaltySlope 0.500000\n",
      "PenaltyCenter 0.000000\n",
      "surfname white\n",
      "GMProjFrac 0.500000\n",
      "WMProjAbs 2.000000\n",
      "lhcostfile (null)\n",
      "rhcostfile (null)\n",
      "interp  trilinear (1)\n",
      "frame  0\n",
      "TolPowell 0.000000\n",
      "nMaxItersPowell 36\n",
      "n1dmin  3\n",
      "Profile   0\n",
      "Gdiag_no  -1\n",
      "AddNoise  0 (0)\n",
      "SynthSeed 1511594245\n",
      "TransRandMax 0.000000\n",
      "RotRandMax 0.000000\n",
      "Translations 0.000000 0.000000 0.000000\n",
      "Rotations   0.000000 0.000000 0.000000\n",
      "Input reg\n",
      " 0.99916   0.04066  -0.00584   1.00740;\n",
      " 0.01571  -0.24672   0.96896  -20.63093;\n",
      "-0.03796   0.96823   0.24715   6.56025;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Loading mov\n",
      "Projecting LH Surfs\n",
      "Loading lh.white surf\n",
      "Loading lh.thickness for GM\n",
      "GM Proj: 1 0.500000 2.000000\n",
      "WM Proj: 0 0.500000 2.000000\n",
      "Projecting RH Surfs\n",
      "Loading rh.white surf\n",
      "Loading rh.thickness for GM\n",
      "Projecting RH Surfs\n",
      "Using lh.cortex.label\n",
      "Using rh.cortex.label\n",
      "Computing relative cost\n",
      " 0  -25.0 -25.0 -25.0   1.017825\n",
      " 1  -25.0 -25.0  25.0   1.016416\n",
      " 2  -25.0  25.0 -25.0   1.036743\n",
      " 3  -25.0  25.0  25.0   1.014733\n",
      " 4   25.0 -25.0 -25.0   1.014024\n",
      " 5   25.0 -25.0  25.0   1.030620\n",
      " 6   25.0  25.0 -25.0   1.037583\n",
      " 7   25.0  25.0  25.0   1.030142\n",
      "REL:  8  0.374483    8.198086  1.024761 rel = 0.365434 \n",
      "Initial costs ----------------\n",
      "Number of surface hits 164297\n",
      "WM  Intensity   746.5978 +/- 117.6816\n",
      "Ctx Intensity   828.1865 +/- 164.2288\n",
      "Pct Contrast      8.9120 +/-  21.4596\n",
      "Cost   0.3745\n",
      "RelCost   0.3654\n",
      "\n",
      "------------------------------------\n",
      "Brute force preopt -0.1 0.1 0.1, n = 729\n",
      "     0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.3754   0.3754  0.0\n",
      "     3  -0.1000  -0.1000  -0.1000  -0.1000   0.0000  -0.1000      0.3738   0.3738  0.0\n",
      "    12  -0.1000  -0.1000  -0.1000   0.0000   0.0000  -0.1000      0.3724   0.3724  0.0\n",
      "   255   0.0000  -0.1000  -0.1000   0.0000   0.0000  -0.1000      0.3717   0.3717  0.0\n",
      "   256   0.0000  -0.1000  -0.1000   0.0000   0.0000   0.0000      0.3716   0.3716  0.0\n",
      "   265   0.0000  -0.1000  -0.1000   0.1000   0.0000   0.0000      0.3712   0.3712  0.0\n",
      "   266   0.0000  -0.1000  -0.1000   0.1000   0.0000   0.1000      0.3710   0.3710  0.0\n",
      "Brute Force --------------------------\n",
      "Min cost was 0.371048\n",
      "Number of iterations   729\n",
      "Search time 0.602000 sec\n",
      "Parameters at best (transmm, rotdeg)\n",
      "  0.000  -0.100  -0.100  0.100  0.000  0.100 \n",
      "--------------------------------------------\n",
      "\n",
      "Starting Powell Minimization\n",
      "Init Powel Params dof = 6\n",
      "0 0\n",
      "1 -0.1\n",
      "2 -0.1\n",
      "3 0.1\n",
      "4 0\n",
      "5 0.1\n",
      "fs_powell::minimize\n",
      "  nparams 6\n",
      "  maxfev 36\n",
      "  ftol   0.000000\n",
      "  linmin_xtol_   0.001000\n",
      "  powell nthiter 0: fret = 0.372982\n",
      "   6  0.382 -0.100 -0.100  0.100  0.000  0.100   0.3702336676\n",
      "   7  0.243 -0.100 -0.100  0.100  0.000  0.100   0.3687594893\n",
      "   9  0.247 -0.100 -0.100  0.100  0.000  0.100   0.3687580105\n",
      "  18  0.247 -0.050 -0.100  0.100  0.000  0.100   0.3684951716\n",
      "  19  0.247 -0.048 -0.100  0.100  0.000  0.100   0.3684894782\n",
      "  31  0.247 -0.048 -0.320  0.100  0.000  0.100   0.3655611397\n",
      "  32  0.247 -0.048 -0.315  0.100  0.000  0.100   0.3655523731\n",
      "  33  0.247 -0.048 -0.305  0.100  0.000  0.100   0.3655441704\n",
      "  34  0.247 -0.048 -0.303  0.100  0.000  0.100   0.3655441154\n",
      "  42  0.247 -0.048 -0.303  0.105  0.000  0.100   0.3655421574\n",
      "  46  0.247 -0.048 -0.303  0.126  0.000  0.100   0.3655369083\n",
      "  48  0.247 -0.048 -0.303  0.118  0.000  0.100   0.3655268065\n",
      "  50  0.247 -0.048 -0.303  0.120  0.000  0.100   0.3655233310\n",
      "  51  0.247 -0.048 -0.303  0.122  0.000  0.100   0.3655208133\n",
      "  53  0.247 -0.048 -0.303  0.121  0.000  0.100   0.3655201548\n",
      "  60  0.247 -0.048 -0.303  0.121  0.120  0.100   0.3645309976\n",
      "  62  0.247 -0.048 -0.303  0.121  0.122  0.100   0.3645307150\n",
      "  63  0.247 -0.048 -0.303  0.121  0.121  0.100   0.3645305607\n",
      "  70  0.247 -0.048 -0.303  0.121  0.121  0.038   0.3644588601\n",
      "  71  0.247 -0.048 -0.303  0.121  0.121  0.055   0.3644498938\n",
      "  72  0.247 -0.048 -0.303  0.121  0.121  0.054   0.3644485490\n",
      "  74  0.247 -0.048 -0.303  0.121  0.121  0.053   0.3644472184\n",
      "  75  0.247 -0.048 -0.303  0.121  0.121  0.052   0.3644457721\n",
      "  powell nthiter 1: fret = 0.364446\n",
      "  83  0.274 -0.048 -0.303  0.121  0.121  0.052   0.3644455727\n",
      "  84  0.260 -0.048 -0.303  0.121  0.121  0.052   0.3644329920\n",
      "  86  0.261 -0.048 -0.303  0.121  0.121  0.052   0.3644329232\n",
      "  95  0.261 -0.051 -0.303  0.121  0.121  0.052   0.3644322136\n",
      "  96  0.261 -0.050 -0.303  0.121  0.121  0.052   0.3644302780\n",
      " 104  0.261 -0.050 -0.316  0.121  0.121  0.052   0.3644157647\n",
      " 113  0.261 -0.050 -0.316  0.100  0.121  0.052   0.3644142502\n",
      " 114  0.261 -0.050 -0.316  0.110  0.121  0.052   0.3644071002\n",
      " 115  0.261 -0.050 -0.316  0.109  0.121  0.052   0.3644056321\n",
      " 116  0.261 -0.050 -0.316  0.106  0.121  0.052   0.3644036906\n",
      " 118  0.261 -0.050 -0.316  0.107  0.121  0.052   0.3644027356\n",
      " 125  0.261 -0.050 -0.316  0.107  0.124  0.052   0.3643998826\n",
      " 126  0.261 -0.050 -0.316  0.107  0.130  0.052   0.3643970373\n",
      " 127  0.261 -0.050 -0.316  0.107  0.131  0.052   0.3643969009\n",
      "  powell nthiter 2: fret = 0.364397\n",
      " 147  0.262 -0.050 -0.316  0.107  0.131  0.052   0.3643968315\n",
      " 155  0.262 -0.046 -0.316  0.107  0.131  0.052   0.3643957765\n",
      " 170  0.262 -0.046 -0.313  0.107  0.131  0.052   0.3643955844\n",
      " 172  0.262 -0.046 -0.314  0.107  0.131  0.052   0.3643954614\n",
      "  powell nthiter 3: fret = 0.364395\n",
      " 218  0.261 -0.046 -0.314  0.107  0.131  0.052   0.3643954445\n",
      "  powell nthiter 4: fret = 0.364395\n",
      "Powell done niters = 4\n",
      "Computing relative cost\n",
      " 0  -25.0 -25.0 -25.0   1.019512\n",
      " 1  -25.0 -25.0  25.0   1.014903\n",
      " 2  -25.0  25.0 -25.0   1.037025\n",
      " 3  -25.0  25.0  25.0   1.018073\n",
      " 4   25.0 -25.0 -25.0   1.012626\n",
      " 5   25.0 -25.0  25.0   1.032154\n",
      " 6   25.0  25.0 -25.0   1.037778\n",
      " 7   25.0  25.0  25.0   1.031014\n",
      "REL:  8  0.364395    8.203085  1.025386 rel = 0.355374 \n",
      "Number of iterations     4\n",
      "Min cost was 0.364395\n",
      "Number of FunctionCalls   342\n",
      "TolPowell 0.000000\n",
      "nMaxItersPowell 36\n",
      "OptimizationTime 13.556000 sec\n",
      "Parameters at optimum (transmm)  0.26134 -0.04552 -0.31425\n",
      "Parameters at optimum (rotdeg)  0.10737  0.13073  0.05169 \n",
      "Final costs ----------------\n",
      "Number of surface hits 164368\n",
      "WM  Intensity   744.2297 +/- 117.5187\n",
      "Ctx Intensity   828.0292 +/- 166.1494\n",
      "Pct Contrast      9.1365 +/-  21.7853\n",
      "Cost   0.3644\n",
      "RelCost   0.3654\n",
      "Reg at min cost was \n",
      " 0.99905   0.04309  -0.00615   1.30224;\n",
      " 0.01668  -0.24850   0.96849  -20.68777;\n",
      "-0.04021   0.96767   0.24898   6.20501;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Writing optimal reg to bold/003/register.dof6.dat, type = 14 \n",
      "Original Reg \n",
      " 0.99916   0.04066  -0.00584   1.00740;\n",
      " 0.01571  -0.24672   0.96896  -20.63093;\n",
      "-0.03796   0.96823   0.24715   6.56025;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Original Reg - Optimal Reg\n",
      " 0.00010  -0.00243   0.00031  -0.29483;\n",
      "-0.00097   0.00178   0.00047   0.05685;\n",
      " 0.00225   0.00056  -0.00183   0.35524;\n",
      " 0.00000   0.00000   0.00000   0.00000;\n",
      "\n",
      "Computing change in lh position\n",
      "LH rmsDiffMean 0.329707\n",
      "Computing change in rh position\n",
      "Surface-RMS-Diff-mm 0.374367 0.088987 0.574585\n",
      "mri_segreg done\n",
      "MinCost: 0.364395 744.229651 828.029202 9.136509 \n",
      "tkregister2_cmdl --mov bold/003/template.nii.gz --reg bold/003/register.dof6.dat --noedit --ltaout bold/003/register.dof6.lta\n",
      "tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl\n",
      "INFO: no target volume specified, assuming FreeSurfer orig volume.\n",
      "target  volume orig\n",
      "movable volume bold/003/template.nii.gz\n",
      "reg file       bold/003/register.dof6.dat\n",
      "LoadVol        0\n",
      "ZeroCRAS       0\n",
      "$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $\n",
      "Diagnostic Level -1\n",
      "---- Input registration matrix --------\n",
      " 0.99905   0.04309  -0.00615   1.30224;\n",
      " 0.01668  -0.24850   0.96849  -20.68777;\n",
      "-0.04021   0.96767   0.24898   6.20501;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "float2int = 0\n",
      "---------------------------------------\n",
      "INFO: loading target /usr/local/freesurfer/subjects/pBrain/mri/orig.mgz\n",
      "Ttarg: --------------------\n",
      "-1.00000   0.00000   0.00000   128.00000;\n",
      " 0.00000   0.00000   1.00000  -128.00000;\n",
      " 0.00000  -1.00000   0.00000   128.00000;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "INFO: loading movable bold/003/template.nii.gz\n",
      "Tmov: --------------------\n",
      "-2.00000   0.00000   0.00000   128.00000;\n",
      " 0.00000   0.00000   2.00000  -40.00000;\n",
      " 0.00000  -2.00000   0.00000   128.00000;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "mkheaderreg = 0, float2int = 0\n",
      "---- Input registration matrix --------\n",
      " 0.99905   0.04309  -0.00615   1.30224;\n",
      " 0.01668  -0.24850   0.96849  -20.68777;\n",
      "-0.04021   0.96767   0.24898   6.20501;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Determinant -1\n",
      "subject = pBrain\n",
      "RegMat ---------------------------\n",
      " 0.99905   0.04309  -0.00615   1.30224;\n",
      " 0.01668  -0.24850   0.96849  -20.68777;\n",
      "-0.04021   0.96767   0.24898   6.20501;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Cleaning up\n",
      " \n",
      "Started at Fri Nov 24 13:01:03 CET 2017 \n",
      "Ended   at Fri Nov 24 13:02:09 CET 2017\n",
      "BBR-Run-Time-Sec 66\n",
      " \n",
      "bbregister Done\n",
      "To check results, run:\n",
      "tkregisterfv --mov bold/003/template.nii.gz --reg bold/003/register.dof6.lta --surfs \n",
      " \n",
      "Fri Nov 24 13:02:09 CET 2017\n",
      "register-sess completed \n",
      "Sess01 Mask ------------------------\n",
      "mkbrainmask-sess -maskstem brain -fsd bold -s Sess01 -d /data/martin/prosopagnosia/landscapes -per-run -update\n",
      "------------------------------------------------\n",
      "/data/martin/prosopagnosia/landscapes/Sess01 \n",
      "Fri Nov 24 13:02:09 CET 2017\n",
      "mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -reg /data/martin/prosopagnosia/landscapes/Sess01/bold/register.dof6.lta -ndil 1 -nerode 0\n",
      "Fri Nov 24 13:02:09 CET 2017\n",
      "\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/landscapes/Sess01/bold\n",
      "/usr/local/freesurfer/fsfast/bin/mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -reg /data/martin/prosopagnosia/landscapes/Sess01/bold/register.dof6.lta -ndil 1 -nerode 0\n",
      "\n",
      "freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c\n",
      "$Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "mri_vol2vol --mov template.nii.gz --reg /data/martin/prosopagnosia/landscapes/Sess01/bold/register.dof6.lta --inv --interp nearest --o masks/brain.nii.gz --targ /usr/local/freesurfer/subjects/pBrain/mri/aparc+aseg.mgz\n",
      "regio_read_register: loading lta\n",
      "\n",
      "Matrix from regfile:\n",
      " 0.99914   0.04092  -0.00700   1.31834;\n",
      " 0.01696  -0.24865   0.96845  -20.82574;\n",
      "-0.03789   0.96773   0.24913   6.02416;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "movvol template.nii.gz\n",
      "targvol /usr/local/freesurfer/subjects/pBrain/mri/aparc+aseg.mgz\n",
      "outvol masks/brain.nii.gz\n",
      "regfile /data/martin/prosopagnosia/landscapes/Sess01/bold/register.dof6.lta\n",
      "invert 1\n",
      "tal    0\n",
      "talres 2\n",
      "regheader 0\n",
      "noresample 0\n",
      "interp  nearest (0)\n",
      "precision  float (3)\n",
      "Gdiag_no  -1\n",
      "Synth      0\n",
      "SynthSeed  1512376712\n",
      "\n",
      "Invert!\n",
      "Inverting registration\n",
      "\n",
      "Final tkRAS-to-tkRAS Matrix is:\n",
      " 0.99914   0.01696  -0.03789  -0.73565;\n",
      " 0.04092  -0.24865   0.96773  -11.06199;\n",
      "-0.00699   0.96845   0.24913   18.67703;\n",
      "-0.00000  -0.00000  -0.00000   1.00000;\n",
      "\n",
      "\n",
      "Vox2Vox Matrix is:\n",
      " 1.99828  -0.07578  -0.03393   6.37456;\n",
      "-0.01399   0.49826  -1.93689   117.06773;\n",
      "-0.08184  -1.93546  -0.49730   255.99121;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Resampling\n",
      "Output registration matrix is identity\n",
      "\n",
      "mri_vol2vol done\n",
      "mri_binarize --i masks/brain.nii.gz --o masks/brain.nii.gz --min 0.5\n",
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/landscapes/Sess01/bold\n",
      "cmdline mri_binarize.bin --i masks/brain.nii.gz --o masks/brain.nii.gz --min 0.5 \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      masks/brain.nii.gz\n",
      "frame      0\n",
      "nErode3d   0\n",
      "nErode2d   0\n",
      "output     masks/brain.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        0.5\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n",
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 100064 values in range\n",
      "Counting number of voxels in first frame\n",
      "Found 100064 voxels in final mask\n",
      "Count: 100064 800512.000000 655360 15.268555\n",
      "mri_binarize done\n",
      "Diliating 1\n",
      "mri_binarize --i masks/brain.nii.gz --min 0.5 --dilate 1 --o masks/brain.nii.gz\n",
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/landscapes/Sess01/bold\n",
      "cmdline mri_binarize.bin --i masks/brain.nii.gz --min 0.5 --dilate 1 --o masks/brain.nii.gz \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      masks/brain.nii.gz\n",
      "frame      0\n",
      "nErode3d   0\n",
      "nErode2d   0\n",
      "output     masks/brain.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        0.5\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n",
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 100064 values in range\n",
      "Dilating 1 voxels in 3d\n",
      "Counting number of voxels in first frame\n",
      "Found 127749 voxels in final mask\n",
      "Count: 127749 1021992.000000 655360 19.492950\n",
      "mri_binarize done\n",
      " \n",
      "Started at Fri Nov 24 13:02:09 CET 2017 \n",
      "Ended   at Fri Nov 24 13:02:10 CET 2017\n",
      "Mkbrainmask-Run-Time-Sec 1\n",
      " \n",
      "mkbrainmask Done\n",
      "mri_binarize --i masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o masks/brain.e3.nii.gz\n",
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/landscapes/Sess01/bold\n",
      "cmdline mri_binarize.bin --i masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o masks/brain.e3.nii.gz \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      masks/brain.nii.gz\n",
      "frame      0\n",
      "nErode3d   3\n",
      "nErode2d   0\n",
      "output     masks/brain.e3.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        0.5\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n",
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 123743 values in range\n",
      "Eroding 3 voxels in 3d\n",
      "Counting number of voxels in first frame\n",
      "Found 68863 voxels in final mask\n",
      "Count: 68863 550904.000000 655360 10.507660\n",
      "mri_binarize done\n",
      "mkbrainmask -i 003/template.nii.gz -o 003/masks/brain.nii.gz -reg /data/martin/prosopagnosia/landscapes/Sess01/bold/003/register.dof6.lta -ndil 1 -nerode 0\n",
      "Fri Nov 24 13:02:11 CET 2017\n",
      "\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/landscapes/Sess01/bold\n",
      "/usr/local/freesurfer/fsfast/bin/mkbrainmask -i 003/template.nii.gz -o 003/masks/brain.nii.gz -reg /data/martin/prosopagnosia/landscapes/Sess01/bold/003/register.dof6.lta -ndil 1 -nerode 0\n",
      "\n",
      "freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c\n",
      "$Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "mri_vol2vol --mov 003/template.nii.gz --reg /data/martin/prosopagnosia/landscapes/Sess01/bold/003/register.dof6.lta --inv --interp nearest --o 003/masks/brain.nii.gz --targ /usr/local/freesurfer/subjects/pBrain/mri/aparc+aseg.mgz\n",
      "regio_read_register: loading lta\n",
      "\n",
      "Matrix from regfile:\n",
      " 0.99905   0.04309  -0.00615   1.30222;\n",
      " 0.01668  -0.24850   0.96849  -20.68777;\n",
      "-0.04021   0.96767   0.24898   6.20499;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "movvol 003/template.nii.gz\n",
      "targvol /usr/local/freesurfer/subjects/pBrain/mri/aparc+aseg.mgz\n",
      "outvol 003/masks/brain.nii.gz\n",
      "regfile /data/martin/prosopagnosia/landscapes/Sess01/bold/003/register.dof6.lta\n",
      "invert 1\n",
      "tal    0\n",
      "talres 2\n",
      "regheader 0\n",
      "noresample 0\n",
      "interp  nearest (0)\n",
      "precision  float (3)\n",
      "Gdiag_no  -1\n",
      "Synth      0\n",
      "SynthSeed  1511716083\n",
      "\n",
      "Invert!\n",
      "Inverting registration\n",
      "\n",
      "Final tkRAS-to-tkRAS Matrix is:\n",
      " 0.99905   0.01668  -0.04021  -0.70644;\n",
      " 0.04309  -0.24850   0.96767  -11.20136;\n",
      "-0.00615   0.96849   0.24898   18.49897;\n",
      "-0.00000  -0.00000  -0.00000   1.00000;\n",
      "\n",
      "\n",
      "Vox2Vox Matrix is:\n",
      " 1.99810  -0.08041  -0.03336   6.64144;\n",
      "-0.01230   0.49796  -1.93698   117.15825;\n",
      "-0.08619  -1.93535  -0.49699   256.11658;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Resampling\n",
      "Output registration matrix is identity\n",
      "\n",
      "mri_vol2vol done\n",
      "mri_binarize --i 003/masks/brain.nii.gz --o 003/masks/brain.nii.gz --min 0.5\n",
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/landscapes/Sess01/bold\n",
      "cmdline mri_binarize.bin --i 003/masks/brain.nii.gz --o 003/masks/brain.nii.gz --min 0.5 \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      003/masks/brain.nii.gz\n",
      "frame      0\n",
      "nErode3d   0\n",
      "nErode2d   0\n",
      "output     003/masks/brain.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        0.5\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 99903 values in range\n",
      "Counting number of voxels in first frame\n",
      "Found 99903 voxels in final mask\n",
      "Count: 99903 799224.000000 655360 15.243988\n",
      "mri_binarize done\n",
      "Diliating 1\n",
      "mri_binarize --i 003/masks/brain.nii.gz --min 0.5 --dilate 1 --o 003/masks/brain.nii.gz\n",
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/landscapes/Sess01/bold\n",
      "cmdline mri_binarize.bin --i 003/masks/brain.nii.gz --min 0.5 --dilate 1 --o 003/masks/brain.nii.gz \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      003/masks/brain.nii.gz\n",
      "frame      0\n",
      "nErode3d   0\n",
      "nErode2d   0\n",
      "output     003/masks/brain.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        0.5\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n",
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 99903 values in range\n",
      "Dilating 1 voxels in 3d\n",
      "Counting number of voxels in first frame\n",
      "Found 127482 voxels in final mask\n",
      "Count: 127482 1019856.000000 655360 19.452209\n",
      "mri_binarize done\n",
      " \n",
      "Started at Fri Nov 24 13:02:11 CET 2017 \n",
      "Ended   at Fri Nov 24 13:02:12 CET 2017\n",
      "Mkbrainmask-Run-Time-Sec 1\n",
      " \n",
      "mkbrainmask Done\n",
      "mri_binarize --i 003/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 003/masks/brain.e3.nii.gz\n",
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/landscapes/Sess01/bold\n",
      "cmdline mri_binarize.bin --i 003/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 003/masks/brain.e3.nii.gz \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      003/masks/brain.nii.gz\n",
      "frame      0\n",
      "nErode3d   3\n",
      "nErode2d   0\n",
      "output     003/masks/brain.e3.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        0.5\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n",
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 123489 values in range\n",
      "Eroding 3 voxels in 3d\n",
      "Counting number of voxels in first frame\n",
      "Found 68745 voxels in final mask\n",
      "Count: 68745 549960.000000 655360 10.489655\n",
      "mri_binarize done\n",
      "meanval --i 003/f.nii --m 003/masks/brain.e3.nii.gz --o 003/global.meanval.dat --avgwf 003/global.waveform.dat\n",
      "Fri Nov 24 13:02:12 CET 2017\n",
      "\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/landscapes/Sess01/bold\n",
      "/usr/local/freesurfer/bin/meanval --i 003/f.nii --m 003/masks/brain.e3.nii.gz --o 003/global.meanval.dat --avgwf 003/global.waveform.dat\n",
      "\n",
      "freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "mri_segstats --seg 003/masks/brain.e3.nii.gz --id 1 --sum /data/martin/prosopagnosia/landscapes/Sess01/bold/003/tmpdir.meanval.23313/blah.23313 --in 003/f.nii --sfavg 003/global.meanval.dat --avgwf 003/global.waveform.dat\n",
      "\n",
      "$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $\n",
      "cwd \n",
      "cmdline mri_segstats --seg 003/masks/brain.e3.nii.gz --id 1 --sum /data/martin/prosopagnosia/landscapes/Sess01/bold/003/tmpdir.meanval.23313/blah.23313 --in 003/f.nii --sfavg 003/global.meanval.dat --avgwf 003/global.waveform.dat \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "UseRobust  0\n",
      "Loading 003/masks/brain.e3.nii.gz\n",
      "Loading 003/f.nii\n",
      "Voxel Volume is 8 mm^3\n",
      "Generating list of segmentation ids\n",
      "Found   1 segmentations\n",
      "Computing statistics for each segmentation\n",
      "\n",
      "Reporting on   1 segmentations\n",
      "Using PrintSegStat\n",
      "Computing spatial average of each frame\n",
      "  0\n",
      "Writing to 003/global.meanval.dat\n",
      "0 825.895\n",
      "Writing to 003/global.waveform.dat\n",
      "mri_segstats done\n",
      "Fri Nov 24 13:02:19 CET 2017\n",
      "mkbrainmask-sess done\n",
      "Sess01 MC -----------------------------\n",
      "mc-sess -fstem f -fmcstem fmcpr -s Sess01 -d /data/martin/prosopagnosia/landscapes -fsd bold -per-run -update\n",
      "Logfile is /data/martin/prosopagnosia/landscapes/log/mc-Sess01-bold.log\n",
      "-------------------------------------------\n",
      "/data/martin/prosopagnosia/landscapes/Sess01 \n",
      "RunList: 003\n",
      "  ------- ************************** -----------\n",
      "  ------- Motion Correcting Run 003 -----------\n",
      "  ------- ************************** -----------\n",
      "sess = Sess01\n",
      "Fri Nov 24 13:02:19 CET 2017\n",
      "mc-afni2 --i 003/f.nii --t 003/template.nii.gz --o 003/fmcpr.nii.gz --mcdat 003/fmcpr.mcdat\n",
      "/data/martin/prosopagnosia/landscapes/Sess01/bold\n",
      "mri_info --nframes --o /tmp/mriinfo.23477 003/template.nii.gz\n",
      "log file is 003/fmcpr.nii.gz.mclog\n",
      "mcdat file is 003/fmcpr.mcdat\n",
      "tmp dir is 003/tmp.mc-afni2.23477\n",
      "#@# --------------------------------\n",
      "/data/martin/prosopagnosia/landscapes/Sess01/bold\n",
      "mri_convert 003/template.nii.gz 003/tmp.mc-afni2.23477/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float\n",
      "mri_convert.bin 003/template.nii.gz 003/tmp.mc-afni2.23477/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float \n",
      "nskip = 0\n",
      "ndrop = 0\n",
      "$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $\n",
      "reading from 003/template.nii.gz...\n",
      "TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00\n",
      "i_ras = (-0.999463, -0.0273032, 0.0181267)\n",
      "j_ras = (0.022681, -0.975511, -0.21878)\n",
      "k_ras = (0.0236561, -0.218251, 0.975606)\n",
      "changing data type from short to float (noscale = 0)...\n",
      "writing to 003/tmp.mc-afni2.23477/tempvol.nii.gz...\n",
      "#@# --------------------------------\n",
      "/data/martin/prosopagnosia/landscapes/Sess01/bold\n",
      "mri_convert 003/f.nii 003/tmp.mc-afni2.23477/invol.nii.gz -odt float\n",
      "mri_convert.bin 003/f.nii 003/tmp.mc-afni2.23477/invol.nii.gz -odt float \n",
      "$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $\n",
      "reading from 003/f.nii...\n",
      "TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00\n",
      "i_ras = (-0.999463, -0.0273032, 0.0181267)\n",
      "j_ras = (0.022681, -0.975511, -0.21878)\n",
      "k_ras = (0.0236561, -0.218251, 0.975606)\n",
      "changing data type from short to float (noscale = 0)...\n",
      "writing to 003/tmp.mc-afni2.23477/invol.nii.gz...\n",
      "#@# --------------------------------\n",
      "/data/martin/prosopagnosia/landscapes/Sess01/bold\n",
      "3dvolreg.afni -verbose -dfile 003/fmcpr.mcdat -1Dmatrix_save 003/fmcpr.mat -base 003/tmp.mc-afni2.23477/tempvol.nii.gz -prefix 003/tmp.mc-afni2.23477/outvol.nii.gz 003/tmp.mc-afni2.23477/invol.nii.gz\n",
      "++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Aug 29 2012) [64-bit]\n",
      "++ Authored by: RW Cox\n",
      "*+ WARNING:   If you are performing spatial transformations on an oblique dset, \n",
      "  such as 003/tmp.mc-afni2.23477/tempvol.nii.gz,\n",
      "  or viewing/combining it with volumes of differing obliquity,\n",
      "  you should consider running: \n",
      "     3dWarp -deoblique \n",
      "  on this and  other oblique datasets in the same session.\n",
      " See 3dWarp -help for details.\n",
      "++ Oblique dataset:003/tmp.mc-afni2.23477/tempvol.nii.gz is 12.706240 degrees from plumb.\n",
      "++ Reading in base dataset 003/tmp.mc-afni2.23477/tempvol.nii.gz\n",
      "++ Oblique dataset:003/tmp.mc-afni2.23477/invol.nii.gz is 12.706240 degrees from plumb.\n",
      "++ Reading input dataset 003/tmp.mc-afni2.23477/invol.nii.gz\n",
      "++ Edging: x=6 y=6 z=2\n",
      "++ Creating mask for -maxdisp\n",
      " + Automask has 123736 voxels\n",
      " + 13998 voxels left in -maxdisp mask after erosion\n",
      "++ Initializing alignment base\n",
      "++ Starting final pass on 167 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..\n",
      "++ CPU time for realignment=0 s  [=0 s/sub-brick]\n",
      "++ Min : roll=-0.294  pitch=-0.123  yaw=-0.078  dS=-0.138  dL=-0.071  dP=-0.288\n",
      "++ Mean: roll=-0.139  pitch=-0.001  yaw=-0.010  dS=+0.022  dL=-0.008  dP=-0.075\n",
      "++ Max : roll=+0.000  pitch=+0.092  yaw=+0.074  dS=+0.143  dL=+0.049  dP=+0.149\n",
      "++ Max displacements (mm) for each sub-brick:\n",
      " 0.32 0.35 0.31 0.39 0.43 0.32 0.34 0.50 0.39 0.48 0.43 0.41 0.45 0.46 0.51 0.18 0.19 0.28 0.23 0.26 0.19 0.20 0.17 0.26 0.16 0.14 0.29 0.17 0.33 0.28 0.28 0.43 0.22 0.25 0.27 0.21 0.22 0.25 0.28 0.16 0.24 0.25 0.17 0.36 0.52 0.39 0.40 0.48 0.36 0.37 0.47 0.34 0.39 0.43 0.39 0.46 0.57 0.36 0.33 0.39 0.46 0.46 0.49 0.54 0.40 0.45 0.43 0.40 0.42 0.49 0.37 0.34 0.38 0.34 0.31 0.30 0.25 0.22 0.24 0.20 0.15 0.19 0.16 0.00 0.32 0.28 0.39 0.33 0.31 0.27 0.48 0.33 0.34 0.28 0.25 0.37 0.27 0.30 0.24 0.18 0.15 0.19 0.26 0.23 0.19 0.17 0.24 0.24 0.21 0.17 0.25 0.20 0.29 0.27 0.21 0.25 0.30 0.24 0.29 0.22 0.24 0.24 0.18 0.15 0.20 0.24 0.26 0.28 0.19 0.24 0.30 0.25 0.26 0.24 0.26 0.25 0.30 0.29 0.33 0.26 0.34 0.31 0.30 0.31 0.25 0.27 0.26 0.29 0.20 0.23 0.24 0.20 0.18 0.17 0.18 0.21 0.20 0.28 0.28 0.34 0.32 0.36 0.40 0.34 0.38 0.42 0.45\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "++ Max displacement in automask = 0.57 (mm) at sub-brick 56\n",
      "++ Wrote dataset to disk in 003/tmp.mc-afni2.23477/outvol.nii.gz\n",
      "#@# --------------------------------\n",
      "/data/martin/prosopagnosia/landscapes/Sess01/bold\n",
      "mri_convert 003/tmp.mc-afni2.23477/outvol.nii.gz 003/fmcpr.nii.gz --in_like 003/template.nii.gz\n",
      "mri_convert.bin 003/tmp.mc-afni2.23477/outvol.nii.gz 003/fmcpr.nii.gz --in_like 003/template.nii.gz \n",
      "reading info from 003/template.nii.gz...\n",
      "$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $\n",
      "reading from 003/tmp.mc-afni2.23477/outvol.nii.gz...\n",
      "TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00\n",
      "INFO: frames are not the same\n",
      "i_ras = (-0.999463, -0.0273032, 0.0181267)\n",
      "j_ras = (0.022681, -0.975511, -0.21878)\n",
      "k_ras = (0.0236561, -0.218251, 0.975606)\n",
      "writing to 003/fmcpr.nii.gz...\n",
      "... cleaning up ....\n",
      "Fri Nov 24 13:04:07 CET 2017\n",
      "mc-afni2 done\n",
      "INFO: Making external regressor from mc params\n",
      "mcdat2mcextreg --i 003/fmcpr.mcdat --o 003/mcprextreg\n",
      "Fri Nov 24 13:04:07 CET 2017\n",
      "\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/landscapes/Sess01/bold\n",
      "/usr/local/freesurfer/fsfast/bin/mcdat2mcextreg --i 003/fmcpr.mcdat --o 003/mcprextreg\n",
      "\n",
      "freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "mri_glmfit --table /data/martin/prosopagnosia/landscapes/Sess01/bold/003/tmpdir.mcdat2extreg.23633/table.dat --glmdir /data/martin/prosopagnosia/landscapes/Sess01/bold/003/tmpdir.mcdat2extreg.23633/glm --osgm --y-out /data/martin/prosopagnosia/landscapes/Sess01/bold/003/tmpdir.mcdat2extreg.23633/y.out.nii --pca\n",
      "\n",
      "$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $\n",
      "cwd /data/martin/prosopagnosia/landscapes/Sess01/bold\n",
      "cmdline mri_glmfit.bin --table /data/martin/prosopagnosia/landscapes/Sess01/bold/003/tmpdir.mcdat2extreg.23633/table.dat --glmdir /data/martin/prosopagnosia/landscapes/Sess01/bold/003/tmpdir.mcdat2extreg.23633/glm --osgm --y-out /data/martin/prosopagnosia/landscapes/Sess01/bold/003/tmpdir.mcdat2extreg.23633/y.out.nii --pca \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "FixVertexAreaFlag = 1\n",
      "UseMaskWithSmoothing     1\n",
      "OneSampleGroupMean 1\n",
      "y    /data/martin/prosopagnosia/landscapes/Sess01/bold/003/tmpdir.mcdat2extreg.23633/table.dat\n",
      "logyflag 0\n",
      "usedti  0\n",
      "glmdir /data/martin/prosopagnosia/landscapes/Sess01/bold/003/tmpdir.mcdat2extreg.23633/glm\n",
      "IllCondOK 0\n",
      "ReScaleX 1\n",
      "DoFFx 0\n",
      "Creating output directory /data/martin/prosopagnosia/landscapes/Sess01/bold/003/tmpdir.mcdat2extreg.23633/glm\n",
      "Loading y from /data/martin/prosopagnosia/landscapes/Sess01/bold/003/tmpdir.mcdat2extreg.23633/table.dat\n",
      "Found 6 data colums\n",
      "Found 167 data rows\n",
      "Saving design matrix to /data/martin/prosopagnosia/landscapes/Sess01/bold/003/tmpdir.mcdat2extreg.23633/glm/Xg.dat\n",
      "Computing normalized matrix\n",
      "Normalized matrix condition is 1\n",
      "Matrix condition is 1\n",
      "search space = 6.000000\n",
      "DOF = 166\n",
      "Starting fit and test\n",
      "Fit completed in 0 minutes\n",
      "Writing results\n",
      "  osgm\n",
      "    maxvox sig=-1e+10  F=726.535  at  index 0 0 0    seed=1512315939\n",
      "Measure:MC                        osgm \n",
      "Tx                                -10000000000.000 \n",
      "Ty                                 -0.070 \n",
      "Tz                                 -2.946 \n",
      "Rx                                  7.128 \n",
      "Ry                                 -7.536 \n",
      "Rz                                -25.094 \n",
      "Computing PCA (167)\n",
      "mri_glmfit done\n",
      "ninputs = 1\n",
      "Checking inputs\n",
      "nframestot = 167\n",
      "Allocing output\n",
      "Done allocing\n",
      "nframes = 167\n",
      "Computing PCA\n",
      "Writing to /data/martin/prosopagnosia/landscapes/Sess01/bold/003/tmpdir.mcdat2extreg.23633/pca.nii\n",
      "mcdat2mcextreg done\n",
      "\n",
      "\n",
      "Fri Nov 24 13:04:07 CET 2017\n",
      "mc-sess completed SUCCESSFULLY\n",
      "Sess01 To Surface -----------------------------\n",
      "rawfunc2surf-sess -fwhm 5 -s Sess01 -d /data/martin/prosopagnosia/landscapes -fsd bold -trgsubject pBrain -update -per-run\n",
      "instem fmcpr\n",
      "outstem fmcpr.sm5.pBrain.hemi\n",
      "------------------------------ \n",
      "1/1 Sess01\n",
      "  1/1 Sess01 003 lh ---------\n",
      "    Fri Nov 24 13:04:07 CET 2017\n",
      "mri_vol2surf --mov /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.nii.gz --reg /data/martin/prosopagnosia/landscapes/Sess01/bold/003/register.dof6.lta --trgsubject pBrain --interp nearest --projfrac 0.5 --hemi lh --o /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.lh.pr.nii.gz --noreshape --cortex\n",
      "srcvol = /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.nii.gz\n",
      "srcreg = /data/martin/prosopagnosia/landscapes/Sess01/bold/003/register.dof6.lta\n",
      "srcregold = 0\n",
      "srcwarp unspecified\n",
      "surf = white\n",
      "hemi = lh\n",
      "trgsubject = pBrain\n",
      "surfreg = sphere.reg\n",
      "ProjFrac = 0.5\n",
      "thickness = thickness\n",
      "reshape = 0\n",
      "interp = nearest\n",
      "float2int = round\n",
      "GetProjMax = 0\n",
      "INFO: float2int code = 0\n",
      "INFO: changing type to float\n",
      "Done loading volume\n",
      "Input reg is LTA\n",
      "-------- original matrix -----------\n",
      " 0.99905   0.04309  -0.00615   1.30222;\n",
      " 0.01668  -0.24850   0.96849  -20.68776;\n",
      "-0.04021   0.96767   0.24898   6.20499;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "-------- original matrix -----------\n",
      "Loading label /usr/local/freesurfer/subjects/pBrain/label/lh.cortex.label\n",
      "Reading surface /usr/local/freesurfer/subjects/pBrain/surf/lh.white\n",
      "Done reading source surface\n",
      "Reading thickness /usr/local/freesurfer/subjects/pBrain/surf/lh.thickness\n",
      "Done\n",
      "Mapping Source Volume onto Source Subject Surface\n",
      " 1 0.5 0.5 0.5\n",
      "using old\n",
      "Done mapping volume to surface\n",
      "Number of source voxels hit = 19539\n",
      "Masking with /usr/local/freesurfer/subjects/pBrain/label/lh.cortex.label\n",
      "Writing to /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.lh.pr.nii.gz\n",
      "Dim: 112635 1 1\n",
      "mri_binarize --i /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.lh.pr.nii.gz --min .00001 --o /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.lh.pr.nii.gz\n",
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/landscapes\n",
      "cmdline mri_binarize.bin --i /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.lh.pr.nii.gz --min .00001 --o /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.lh.pr.nii.gz \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.lh.pr.nii.gz\n",
      "frame      0\n",
      "nErode3d   0\n",
      "nErode2d   0\n",
      "output     /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.lh.pr.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        1e-05\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n",
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 83318 values in range\n",
      "Counting number of voxels in first frame\n",
      "Found 83318 voxels in final mask\n",
      "Count: 83318 83318.000000 112635 73.971678\n",
      "mri_binarize done\n",
      "mri_concat --o /data/martin/prosopagnosia/landscapes/Sess01/bold/masks/brain.pBrain.lh.pr.nii.gz --mean /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.lh.pr.nii.gz\n",
      "ninputs = 1\n",
      "Checking inputs\n",
      "nframestot = 1\n",
      "Allocing output\n",
      "Done allocing\n",
      "nframes = 1\n",
      "Computing mean across frames\n",
      "Writing to /data/martin/prosopagnosia/landscapes/Sess01/bold/masks/brain.pBrain.lh.pr.nii.gz\n",
      "mri_binarize --i /data/martin/prosopagnosia/landscapes/Sess01/bold/masks/brain.pBrain.lh.pr.nii.gz --min 10e-10 --o /data/martin/prosopagnosia/landscapes/Sess01/bold/masks/brain.pBrain.lh.pr.nii.gz\n",
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/landscapes\n",
      "cmdline mri_binarize.bin --i /data/martin/prosopagnosia/landscapes/Sess01/bold/masks/brain.pBrain.lh.pr.nii.gz --min 10e-10 --o /data/martin/prosopagnosia/landscapes/Sess01/bold/masks/brain.pBrain.lh.pr.nii.gz \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      /data/martin/prosopagnosia/landscapes/Sess01/bold/masks/brain.pBrain.lh.pr.nii.gz\n",
      "frame      0\n",
      "nErode3d   0\n",
      "nErode2d   0\n",
      "output     /data/martin/prosopagnosia/landscapes/Sess01/bold/masks/brain.pBrain.lh.pr.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        1e-09\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n",
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 83318 values in range\n",
      "Counting number of voxels in first frame\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found 83318 voxels in final mask\n",
      "Count: 83318 83318.000000 112635 73.971678\n",
      "mri_binarize done\n",
      "  1/1 Sess01 003 rh ---------\n",
      "    Fri Nov 24 13:04:08 CET 2017\n",
      "mri_vol2surf --mov /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.nii.gz --reg /data/martin/prosopagnosia/landscapes/Sess01/bold/003/register.dof6.lta --trgsubject pBrain --interp nearest --projfrac 0.5 --hemi rh --o /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.rh.pr.nii.gz --noreshape --cortex\n",
      "srcvol = /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.nii.gz\n",
      "srcreg = /data/martin/prosopagnosia/landscapes/Sess01/bold/003/register.dof6.lta\n",
      "srcregold = 0\n",
      "srcwarp unspecified\n",
      "surf = white\n",
      "hemi = rh\n",
      "trgsubject = pBrain\n",
      "surfreg = sphere.reg\n",
      "ProjFrac = 0.5\n",
      "thickness = thickness\n",
      "reshape = 0\n",
      "interp = nearest\n",
      "float2int = round\n",
      "GetProjMax = 0\n",
      "INFO: float2int code = 0\n",
      "INFO: changing type to float\n",
      "Done loading volume\n",
      "Input reg is LTA\n",
      "-------- original matrix -----------\n",
      " 0.99905   0.04309  -0.00615   1.30222;\n",
      " 0.01668  -0.24850   0.96849  -20.68776;\n",
      "-0.04021   0.96767   0.24898   6.20499;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "-------- original matrix -----------\n",
      "Loading label /usr/local/freesurfer/subjects/pBrain/label/rh.cortex.label\n",
      "Reading surface /usr/local/freesurfer/subjects/pBrain/surf/rh.white\n",
      "Done reading source surface\n",
      "Reading thickness /usr/local/freesurfer/subjects/pBrain/surf/rh.thickness\n",
      "Done\n",
      "Mapping Source Volume onto Source Subject Surface\n",
      " 1 0.5 0.5 0.5\n",
      "using old\n",
      "Done mapping volume to surface\n",
      "Number of source voxels hit = 19236\n",
      "Masking with /usr/local/freesurfer/subjects/pBrain/label/rh.cortex.label\n",
      "Writing to /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.rh.pr.nii.gz\n",
      "Dim: 111586 1 1\n",
      "mri_binarize --i /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.rh.pr.nii.gz --min .00001 --o /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.rh.pr.nii.gz\n",
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/landscapes\n",
      "cmdline mri_binarize.bin --i /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.rh.pr.nii.gz --min .00001 --o /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.rh.pr.nii.gz \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.rh.pr.nii.gz\n",
      "frame      0\n",
      "nErode3d   0\n",
      "nErode2d   0\n",
      "output     /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.rh.pr.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        1e-05\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n",
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 82503 values in range\n",
      "Counting number of voxels in first frame\n",
      "Found 82503 voxels in final mask\n",
      "Count: 82503 82503.000000 111586 73.936695\n",
      "mri_binarize done\n",
      "mri_concat --o /data/martin/prosopagnosia/landscapes/Sess01/bold/masks/brain.pBrain.rh.pr.nii.gz --mean /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.rh.pr.nii.gz\n",
      "ninputs = 1\n",
      "Checking inputs\n",
      "nframestot = 1\n",
      "Allocing output\n",
      "Done allocing\n",
      "nframes = 1\n",
      "Computing mean across frames\n",
      "Writing to /data/martin/prosopagnosia/landscapes/Sess01/bold/masks/brain.pBrain.rh.pr.nii.gz\n",
      "mri_binarize --i /data/martin/prosopagnosia/landscapes/Sess01/bold/masks/brain.pBrain.rh.pr.nii.gz --min 10e-10 --o /data/martin/prosopagnosia/landscapes/Sess01/bold/masks/brain.pBrain.rh.pr.nii.gz\n",
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/landscapes\n",
      "cmdline mri_binarize.bin --i /data/martin/prosopagnosia/landscapes/Sess01/bold/masks/brain.pBrain.rh.pr.nii.gz --min 10e-10 --o /data/martin/prosopagnosia/landscapes/Sess01/bold/masks/brain.pBrain.rh.pr.nii.gz \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      /data/martin/prosopagnosia/landscapes/Sess01/bold/masks/brain.pBrain.rh.pr.nii.gz\n",
      "frame      0\n",
      "nErode3d   0\n",
      "nErode2d   0\n",
      "output     /data/martin/prosopagnosia/landscapes/Sess01/bold/masks/brain.pBrain.rh.pr.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        1e-09\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n",
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 82503 values in range\n",
      "Counting number of voxels in first frame\n",
      "Found 82503 voxels in final mask\n",
      "Count: 82503 82503.000000 111586 73.936695\n",
      "mri_binarize done\n",
      "  1/1 Sess01 003 lh ---------\n",
      "    Fri Nov 24 13:04:09 CET 2017\n",
      "mri_vol2surf --mov /data/martin/prosopagnosia/landscapes/Sess01/bold/003/fmcpr.nii.gz --reg /data/martin/prosopagnosia/landscapes/Sess01/bold/003/register.dof6.lta --trgsubject pBrain --interp trilin --projfrac 0.5 --hemi lh --o /data/martin/prosopagnosia/landscapes/Sess01/bold/003/fmcpr.sm5.pBrain.lh.nii.gz --noreshape --cortex\n",
      "srcvol = /data/martin/prosopagnosia/landscapes/Sess01/bold/003/fmcpr.nii.gz\n",
      "srcreg = /data/martin/prosopagnosia/landscapes/Sess01/bold/003/register.dof6.lta\n",
      "srcregold = 0\n",
      "srcwarp unspecified\n",
      "surf = white\n",
      "hemi = lh\n",
      "trgsubject = pBrain\n",
      "surfreg = sphere.reg\n",
      "ProjFrac = 0.5\n",
      "thickness = thickness\n",
      "reshape = 0\n",
      "interp = trilin\n",
      "float2int = round\n",
      "GetProjMax = 0\n",
      "INFO: float2int code = 0\n",
      "Done loading volume\n",
      "Input reg is LTA\n",
      "-------- original matrix -----------\n",
      " 0.99905   0.04309  -0.00615   1.30222;\n",
      " 0.01668  -0.24850   0.96849  -20.68776;\n",
      "-0.04021   0.96767   0.24898   6.20499;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "-------- original matrix -----------\n",
      "Loading label /usr/local/freesurfer/subjects/pBrain/label/lh.cortex.label\n",
      "Reading surface /usr/local/freesurfer/subjects/pBrain/surf/lh.white\n",
      "Done reading source surface\n",
      "Reading thickness /usr/local/freesurfer/subjects/pBrain/surf/lh.thickness\n",
      "Done\n",
      "Mapping Source Volume onto Source Subject Surface\n",
      " 1 0.5 0.5 0.5\n",
      "using old\n",
      "Done mapping volume to surface\n",
      "Number of source voxels hit = 19539\n",
      "Masking with /usr/local/freesurfer/subjects/pBrain/label/lh.cortex.label\n",
      "Writing to /data/martin/prosopagnosia/landscapes/Sess01/bold/003/fmcpr.sm5.pBrain.lh.nii.gz\n",
      "Dim: 112635 1 1\n",
      "mris_fwhm --s pBrain --hemi lh --smooth-only --i /data/martin/prosopagnosia/landscapes/Sess01/bold/003/fmcpr.sm5.pBrain.lh.nii.gz --fwhm 5 --o /data/martin/prosopagnosia/landscapes/Sess01/bold/003/fmcpr.sm5.pBrain.lh.nii.gz --mask /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.lh.nii.gz --no-detrend\n",
      "pBrain lh white\n",
      "Number of vertices 112635\n",
      "Number of faces    225266\n",
      "Total area         74093.468750\n",
      "GroupSurface 0\n",
      "AvgVtxArea       0.657819\n",
      "AvgVtxDist       0.887337\n",
      "StdVtxDist       0.259981\n",
      "Loading mask /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.lh.nii.gz\n",
      "Found 83318 voxels in mask\n",
      "Not Polynomial detrending\n",
      "Smoothing input by fwhm=5.000000, gstd=2.123305, niters=14 \n",
      "Only smoothing, so saving and exiting now\n",
      "  1/1 Sess01 003 rh ---------\n",
      "    Fri Nov 24 13:04:26 CET 2017\n",
      "mri_vol2surf --mov /data/martin/prosopagnosia/landscapes/Sess01/bold/003/fmcpr.nii.gz --reg /data/martin/prosopagnosia/landscapes/Sess01/bold/003/register.dof6.lta --trgsubject pBrain --interp trilin --projfrac 0.5 --hemi rh --o /data/martin/prosopagnosia/landscapes/Sess01/bold/003/fmcpr.sm5.pBrain.rh.nii.gz --noreshape --cortex\n",
      "srcvol = /data/martin/prosopagnosia/landscapes/Sess01/bold/003/fmcpr.nii.gz\n",
      "srcreg = /data/martin/prosopagnosia/landscapes/Sess01/bold/003/register.dof6.lta\n",
      "srcregold = 0\n",
      "srcwarp unspecified\n",
      "surf = white\n",
      "hemi = rh\n",
      "trgsubject = pBrain\n",
      "surfreg = sphere.reg\n",
      "ProjFrac = 0.5\n",
      "thickness = thickness\n",
      "reshape = 0\n",
      "interp = trilin\n",
      "float2int = round\n",
      "GetProjMax = 0\n",
      "INFO: float2int code = 0\n",
      "Done loading volume\n",
      "Input reg is LTA\n",
      "-------- original matrix -----------\n",
      " 0.99905   0.04309  -0.00615   1.30222;\n",
      " 0.01668  -0.24850   0.96849  -20.68776;\n",
      "-0.04021   0.96767   0.24898   6.20499;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "-------- original matrix -----------\n",
      "Loading label /usr/local/freesurfer/subjects/pBrain/label/rh.cortex.label\n",
      "Reading surface /usr/local/freesurfer/subjects/pBrain/surf/rh.white\n",
      "Done reading source surface\n",
      "Reading thickness /usr/local/freesurfer/subjects/pBrain/surf/rh.thickness\n",
      "Done\n",
      "Mapping Source Volume onto Source Subject Surface\n",
      " 1 0.5 0.5 0.5\n",
      "using old\n",
      "Done mapping volume to surface\n",
      "Number of source voxels hit = 19236\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Masking with /usr/local/freesurfer/subjects/pBrain/label/rh.cortex.label\n",
      "Writing to /data/martin/prosopagnosia/landscapes/Sess01/bold/003/fmcpr.sm5.pBrain.rh.nii.gz\n",
      "Dim: 111586 1 1\n",
      "mris_fwhm --s pBrain --hemi rh --smooth-only --i /data/martin/prosopagnosia/landscapes/Sess01/bold/003/fmcpr.sm5.pBrain.rh.nii.gz --fwhm 5 --o /data/martin/prosopagnosia/landscapes/Sess01/bold/003/fmcpr.sm5.pBrain.rh.nii.gz --mask /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.rh.nii.gz --no-detrend\n",
      "pBrain rh white\n",
      "Number of vertices 111586\n",
      "Number of faces    223168\n",
      "Total area         73917.976562\n",
      "GroupSurface 0\n",
      "AvgVtxArea       0.662431\n",
      "AvgVtxDist       0.889571\n",
      "StdVtxDist       0.264496\n",
      "Loading mask /data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.rh.nii.gz\n",
      "Found 82503 voxels in mask\n",
      "Not Polynomial detrending\n",
      "Smoothing input by fwhm=5.000000, gstd=2.123305, niters=14 \n",
      "Only smoothing, so saving and exiting now\n",
      "\n",
      "Fri Nov 24 13:04:42 CET 2017\n",
      "rawfunc2surf-sess completed \n",
      "----------------------------------------\n",
      "Started at Fri Nov 24 12:59:30 CET 2017\n",
      "Ended   at Fri Nov 24 13:04:42 CET 2017\n",
      "preproc-sess done\n"
     ]
    }
   ],
   "source": [
    "preproc-sess -sf sessids -surface pBrain lhrh -fwhm 5 -per-run -fsd bold"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[34;42m/data/martin/prosopagnosia/landscapes\u001b[00m\n",
      "├── \u001b[34;42mlog\u001b[00m\n",
      "│   ├── \u001b[01;32mmc-Sess01-bold.log\u001b[00m\n",
      "│   ├── \u001b[01;32mmkbrainmask-Sess01-bold.log\u001b[00m\n",
      "│   ├── \u001b[01;32mmktemplate-sess.Sess01.bold.f.log\u001b[00m\n",
      "│   ├── \u001b[01;32mpreproc-Sess01-bold.log\u001b[00m\n",
      "│   ├── \u001b[01;32mpreproc-sess.Sess01.log\u001b[00m\n",
      "│   ├── \u001b[01;32mrawfunc2surf-sess.Sess01.bold.fmcpr.sm5.pBrain.lhrh.log\u001b[00m\n",
      "│   └── \u001b[01;32mregister-sess.Sess01.log\u001b[00m\n",
      "├── \u001b[34;42mSess01\u001b[00m\n",
      "│   ├── \u001b[34;42mbold\u001b[00m\n",
      "│   │   ├── \u001b[34;42m003\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mf-infodump.dat\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mfmcpr.mat.aff12.1D\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mfmcpr.mcdat\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mfmcpr.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mfmcpr.nii.gz.mclog\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mfmcpr.sm5.pBrain.lh.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mfmcpr.sm5.pBrain.rh.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mf.nii\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mglobal.meanval.dat\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mglobal.waveform.dat\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32minit.register.dof6.dat\u001b[00m\n",
      "│   │   │   ├── \u001b[34;42mmasks\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mbrain.e3.nii.gz\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mbrain.nii.gz\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mbrain.nii.gz.mkbrainmask.log\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mbrain.pBrain.lh.nii.gz\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mbrain.pBrain.lh.pr.nii.gz\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mbrain.pBrain.rh.nii.gz\u001b[00m\n",
      "│   │   │   │   └── \u001b[01;32mbrain.pBrain.rh.pr.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mmcdat2extreg.log\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mmcprextreg\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mregister.dof6.dat~\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mregister.dof6.dat.log\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mregister.dof6.dat.mincost\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mregister.dof6.dat.param\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mregister.dof6.dat.sum\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mregister.dof6.lta\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mtemplate.log\u001b[00m\n",
      "│   │   │   └── \u001b[01;32mtemplate.nii.gz\u001b[00m\n",
      "│   │   ├── \u001b[01;32minit.register.dof6.dat\u001b[00m\n",
      "│   │   ├── \u001b[34;42mmasks\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mbrain.e3.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mbrain.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mbrain.nii.gz.mkbrainmask.log\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mbrain.pBrain.lh.pr.nii.gz\u001b[00m\n",
      "│   │   │   └── \u001b[01;32mbrain.pBrain.rh.pr.nii.gz\u001b[00m\n",
      "│   │   ├── \u001b[01;32mregister.dof6.dat~\u001b[00m\n",
      "│   │   ├── \u001b[01;32mregister.dof6.dat.log\u001b[00m\n",
      "│   │   ├── \u001b[01;32mregister.dof6.dat.mincost\u001b[00m\n",
      "│   │   ├── \u001b[01;32mregister.dof6.dat.param\u001b[00m\n",
      "│   │   ├── \u001b[01;32mregister.dof6.dat.sum\u001b[00m\n",
      "│   │   ├── \u001b[01;32mregister.dof6.lta\u001b[00m\n",
      "│   │   ├── \u001b[01;32mtemplate.log\u001b[00m\n",
      "│   │   └── \u001b[01;32mtemplate.nii.gz\u001b[00m\n",
      "│   ├── \u001b[01;32mdcmunpack.log\u001b[00m\n",
      "│   ├── \u001b[01;32mimagelist.dat\u001b[00m\n",
      "│   ├── \u001b[01;32mseries-info.dat\u001b[00m\n",
      "│   └── \u001b[01;32msubjectname\u001b[00m\n",
      "└── \u001b[01;32msessids\u001b[00m\n",
      "\n",
      "6 directories, 54 files\n"
     ]
    }
   ],
   "source": [
    "tree ${projectDir}landscapes"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "show some quality checks"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "#plot-twf-sess -s Sess01 -fsd bold -mc"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "#tkregister-sess -s Sess01 -fsd bold -per-run"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### specify design"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "add onset files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\t0\t30\t1\n",
      "30\t1\t30\t1\n",
      "60\t0\t30\t1\n",
      "90\t1\t30\t1\n",
      "120\t0\t30\t1\n",
      "150\t1\t30\t1\n",
      "180\t0\t30\t1\n",
      "210\t1\t30\t1\n",
      "240\t0\t30\t1\n",
      "270\t1\t30\t1\n",
      "300\t0\t30\t1\n",
      "330\t1\t30\t1\n",
      "360\t0\t30\t1\n",
      "390\t1\t30\t1\n",
      "420\t0\t30\t1\n",
      "450\t1\t30\t1\n"
     ]
    }
   ],
   "source": [
    "cp ${projectDir}design/landscapeDesign.par ./Sess01/bold/003/design.par\n",
    "cat Sess01/bold/003/design.par"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "mkanalysis-sess\n",
    "\n",
    "- mcextreg: Use movement as nuisance regressor\n",
    "- event-related: can be used for blocked designs too\n",
    "- nskip: ignore first n scans (we already removed them)\n",
    "- nconditions: because there is always a 0 baseline, two conditions equals 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting TER to 0.050000\n",
      "Setting TimeWindow to 40.000000\n",
      "Setting PreStim    to 0\n",
      "Setting PostStim   to 40.000000\n",
      "# FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c\n",
      "# MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $\n",
      "# MKACMD /usr/local/freesurfer/fsfast/bin/mkanalysis-sess -analysis design.sm5.rh -surface pBrain rh -fwhm 5 -per-run -fsd bold -paradigm design.par -event-related -spmhrf 0 -refeventdur 30 -polyfit 2 -mcextreg -nskip 0 -TR 3 -nconditions 1\n",
      "# DATE Fri Nov 24 13:04:43 CET 2017\n",
      "\n",
      "analysis design.sm5.rh\n",
      "mcstem fmcpr\n",
      "fsd bold\n",
      "TR 3\n",
      "RegDOF 6\n",
      "PerSession 0\n",
      "RawSpace surface pBrain rh\n",
      "mask brain\n",
      "RawFWHM 5\n",
      "RawSTC none\n",
      "nSliceGroups 1\n",
      "UseB0DC 0\n",
      "ApplySubCortMask 1\n",
      "inorm 100\n",
      "acfbins 30\n",
      "fixacf  1\n",
      "acffwhm 20\n",
      "acfsvd  0\n",
      "designtype event-related\n",
      "nskip 0\n",
      "polyfit 2\n",
      "HPFCutoffHz 0\n",
      "HeteroGCor 0\n",
      "nconditions 1\n",
      "parname design.par\n",
      "RefEventDur 30\n",
      "timewindow 40.000000\n",
      "prestim 0\n",
      "TER 0.050000\n",
      "spmhrf 0\n",
      "stimulusdelay -1.50000000000000000000\n",
      "Condition 1 Condition01\n",
      "nuisreg mcprextreg 3\n",
      "mkanalysis-sess done\n"
     ]
    }
   ],
   "source": [
    "hemi=\"rh\"\n",
    "\n",
    "mkanalysis-sess -analysis design.sm5.${hemi} \\\n",
    "-surface pBrain ${hemi} \\\n",
    "-fwhm 5 \\\n",
    "-per-run \\\n",
    "-fsd bold \\\n",
    "-paradigm design.par \\\n",
    "-event-related \\\n",
    "-spmhrf 0 \\\n",
    "-refeventdur 30 \\\n",
    "-polyfit 2 \\\n",
    "-mcextreg \\\n",
    "-nskip 0 \\\n",
    "-TR 3 \\\n",
    "-nconditions 1"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### contrast"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "INFO: Found 1 Non-Null Conditions\n",
      "INFO: Found 1 Delays\n",
      "Condition Weights: 1.00000000000000000000\n",
      "mkcontrast2 -config design.sm5.rh/act-vs-rest.config -anadir design.sm5.rh -wcond 1.00000000000000000000 -sumconds -o design.sm5.rh/act-vs-rest.mat -wdelay 1 -no-octave\n",
      "  $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $\n",
      "cmtxfile  design.sm5.rh/act-vs-rest.mat\n",
      "nconds    1,  wcond  1.00000000000000000000\n",
      "ndelays   1, wdelay 1\n",
      "ndelays   1, wpsa   \n",
      "sumconds  1\n",
      "sumdelays 0\n",
      "nircorr   0\n",
      "TER       0.050000\n",
      "rdelta    \n",
      "rtau      \n",
      "  cmtxfile  design.sm5.rh/act-vs-rest.mat\n",
      "  monly  0\n",
      "  NCond   1\n",
      "  WCond   1.00000000000000000000\n",
      "  NDelay  1\n",
      "  WDelay  1\n",
      "  TER         0.050000\n",
      "  sumconds   1\n",
      "  sumdelays  0\n",
      "  nircorr  0\n",
      "  TPreStim  0\n",
      "  RmPreStim  0\n",
      "  rdelta     0 0\n",
      "  rtau       0 0\n",
      "  ndelays    1\n",
      "  CNorm      1\n",
      "  setwdelay  0\n",
      "  setwcond   0\n",
      "Matlab file is /tmp/mkcontrast2.24158.m\n",
      "MATLAB is selecting SOFTWARE OPENGL rendering.\n",
      "\n",
      "                            < M A T L A B (R) >\n",
      "                  Copyright 1984-2016 The MathWorks, Inc.\n",
      "                   R2016a (9.0.0.341360) 64-bit (glnxa64)\n",
      "                             February 11, 2016\n",
      "\n",
      " \n",
      "To get started, type one of these: helpwin, helpdesk, or demo.\n",
      "For product information, visit www.mathworks.com.\n",
      " \n",
      "\n",
      "\tThis is a Classroom License for instructional use only.\n",
      "\tResearch and commercial use is prohibited.\n",
      "\n",
      ">> starting mkcontrast2m\n",
      "Normalizing contrast matrix\n",
      "mkcontrast2m done\n",
      ">> Fri Nov 24 13:04:51 CET 2017\n"
     ]
    }
   ],
   "source": [
    "mkcontrast-sess -analysis design.sm5.${hemi} -contrast act-vs-rest -a 1 -c 0"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### estimate"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Surface data pBrain rh\n",
      "--------------------------------------------------------------\n",
      "selxavg3-sess logfile is /data/martin/prosopagnosia/landscapes/log/selxavg3-sess-bold-design.sm5.rh-171124130451.log\n",
      "--------------------------------------------------------------\n",
      "selxavg3-sess log file\n",
      "/usr/local/freesurfer/fsfast/bin/selxavg3-sess\n",
      "-sf sessids -analysis design.sm5.rh\n",
      "$Id: selxavg3-sess,v 1.68 2016/05/10 03:24:18 greve Exp $\n",
      "uid=1000(martin) gid=1000(martin) groups=1000(martin),24(cdrom),25(floppy),29(audio),30(dip),44(video),46(plugdev),108(netdev),110(lpadmin),113(scanner),117(bluetooth),999(docker)\n",
      "/data/martin/prosopagnosia/landscapes\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "Fri Nov 24 13:04:51 CET 2017\n",
      "preproc-sess -s Sess01 -d /data/martin/prosopagnosia/landscapes -a design.sm5.rh -nolog\n",
      "--------------------------------------------------------------\n",
      "preproc-sess logfile is /dev/null\n",
      "--------------------------------------------------------------\n",
      "$Id: preproc-sess,v 1.64.2.1 2016/08/02 21:19:09 greve Exp $\n",
      "martin\n",
      "setenv FREESURFER_HOME /usr/local/freesurfer\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "/data/martin/prosopagnosia/landscapes\n",
      "/usr/local/freesurfer/fsfast/bin/preproc-sess\n",
      "-s Sess01 -d /data/martin/prosopagnosia/landscapes -a design.sm5.rh -nolog\n",
      "Fri Nov 24 13:04:52 CET 2017\n",
      "instem   f \n",
      "mc   1     f fmcpr \n",
      "stc  0     fmcpr\n",
      "sm   0   \n",
      "mask 1   brain\n",
      "Sess01 Template -----------------------------\n",
      "mktemplate-sess -s Sess01 -d /data/martin/prosopagnosia/landscapes -fsd bold -nolog -update\n",
      " \n",
      "Session: /data/martin/prosopagnosia/landscapes/Sess01 ----------------\n",
      "Fri Nov 24 13:04:52 CET 2017\n",
      "Detected input format at nii\n",
      "Sess01 Update not needed\n",
      "  Run: 003 ----------------\n",
      "  Fri Nov 24 13:04:52 CET 2017\n",
      "  Sess01 003 Update not needed\n",
      "Fri Nov 24 13:04:52 CET 2017\n",
      "mktemplate-sess completed \n",
      "Sess01 Registration -----------------------------\n",
      "register-sess -s Sess01 -d /data/martin/prosopagnosia/landscapes -fsd bold -delete-dat -dof 6 -bold -per-run -nolog -update -init-coreg\n",
      "--------------------------------------------------------------\n",
      "register-sess logfile is /dev/null\n",
      "--------------------------------------------------------------\n",
      "Fri Nov 24 13:04:52 CET 2017\n",
      "\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/landscapes\n",
      "/usr/local/freesurfer/fsfast/bin/register-sess -s Sess01 -d /data/martin/prosopagnosia/landscapes -fsd bold -delete-dat -dof 6 -bold -per-run -nolog -update -init-coreg\n",
      "\n",
      "freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      " \n",
      "Session: /data/martin/prosopagnosia/landscapes/Sess01 ----------------\n",
      "Fri Nov 24 13:04:52 CET 2017\n",
      "/data/martin/prosopagnosia/landscapes/Sess01\n",
      "  Run: 003 ----------------\n",
      "Fri Nov 24 13:04:52 CET 2017\n",
      "Update not needed\n",
      "Fri Nov 24 13:04:52 CET 2017\n",
      "register-sess completed \n",
      "Sess01 Mask ------------------------\n",
      "mkbrainmask-sess -maskstem brain -fsd bold -s Sess01 -d /data/martin/prosopagnosia/landscapes -per-run -nolog -update\n",
      "------------------------------------------------\n",
      "/data/martin/prosopagnosia/landscapes/Sess01 \n",
      "Fri Nov 24 13:04:52 CET 2017\n",
      "Sess01 Update not needed for session-level mask\n",
      "Sess01 Update not needed for run 003 mask\n",
      "Sess01 Update not needed for run 003 meanval\n",
      "Fri Nov 24 13:04:52 CET 2017\n",
      "mkbrainmask-sess done\n",
      "Sess01 MC -----------------------------\n",
      "mc-sess -fstem f -fmcstem fmcpr -s Sess01 -d /data/martin/prosopagnosia/landscapes -fsd bold -per-run -nolog -update\n",
      "Logfile is /dev/null\n",
      "-------------------------------------------\n",
      "/data/martin/prosopagnosia/landscapes/Sess01 \n",
      "RunList: 003\n",
      "Sess01 003 Update not needed\n",
      "\n",
      "\n",
      "Fri Nov 24 13:04:52 CET 2017\n",
      "mc-sess completed SUCCESSFULLY\n",
      "Sess01 To Surface -----------------------------\n",
      "rawfunc2surf-sess -fwhm 5 -s Sess01 -d /data/martin/prosopagnosia/landscapes -fsd bold -hemi rh -trgsubject pBrain -nolog -update -per-run\n",
      "instem fmcpr\n",
      "outstem fmcpr.sm5.pBrain.hemi\n",
      "------------------------------ \n",
      "1/1 Sess01\n",
      "  1/1 Sess01 003 rh ---------\n",
      "    Fri Nov 24 13:04:52 CET 2017\n",
      "/data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.rh.pr.nii.gz does not need updating\n",
      "/data/martin/prosopagnosia/landscapes/Sess01/bold/masks/brain.pBrain.rh.pr.nii.gz does not need updating\n",
      "  1/1 Sess01 003 rh ---------\n",
      "    Fri Nov 24 13:04:52 CET 2017\n",
      "    Sess01 003 Update not needed\n",
      "\n",
      "Fri Nov 24 13:04:52 CET 2017\n",
      "rawfunc2surf-sess completed \n",
      "----------------------------------------\n",
      "Started at Fri Nov 24 13:04:52 CET 2017\n",
      "Ended   at Fri Nov 24 13:04:52 CET 2017\n",
      "preproc-sess done\n",
      "-------------------------------------------\n",
      "1/1 /data/martin/prosopagnosia/landscapes/Sess01 \n",
      "Fri Nov 24 13:04:52 CET 2017\n",
      "anadir = /data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.rh\n",
      "DoGLMFit = 1\n",
      "DoContrasts = 1\n",
      "UpdateNeeded = 1\n",
      "    Sess01 Update needed\n",
      "/data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.rh/sxa3.config.txt\n",
      "MLF is /tmp/selxavg3-sess-24475.m\n",
      "------------------------------------------\n",
      "% Fri Nov 24 13:04:52 CET 2017  \n",
      "% /data/martin/prosopagnosia/landscapes  \n",
      "%  design.sm5.rh  \n",
      "which fast_selxavg3\n",
      "which fast_ldanaflac\n",
      "which MRIread\n",
      "  \n",
      "  \n",
      "fast_selxavg3b('/data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.rh/sxa3.config.txt')\n",
      "if(~fast_fileexists('/tmp/selxavg3-sess-24475.ok')); quit; end\n",
      "%--------------------------------\n",
      "  \n",
      "  \n",
      "quit;\n",
      "------------------------------------------\n",
      "------------------------------------------\n",
      "------- matlab output --------------------\n",
      "MATLAB is selecting SOFTWARE OPENGL rendering.\n",
      "\n",
      "                            < M A T L A B (R) >\n",
      "                  Copyright 1984-2016 The MathWorks, Inc.\n",
      "                   R2016a (9.0.0.341360) 64-bit (glnxa64)\n",
      "                             February 11, 2016\n",
      "\n",
      " \n",
      "To get started, type one of these: helpwin, helpdesk, or demo.\n",
      "For product information, visit www.mathworks.com.\n",
      " \n",
      "\n",
      "\tThis is a Classroom License for instructional use only.\n",
      "\tResearch and commercial use is prohibited.\n",
      "\n",
      ">> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m\n",
      ">> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m\n",
      ">> /usr/local/freesurfer/matlab/MRIread.m\n",
      ">> >> >> starting fast_selxavg3b\n",
      "\n",
      "\n",
      "#@# Sess01 ###############################\n",
      "/data/martin/prosopagnosia/landscapes/Sess01\n",
      "-------------------------\n",
      "$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $\n",
      "-------------------------\n",
      "outtop = /data/martin/prosopagnosia/landscapes\n",
      "Extension format = nii.gz\n",
      "INFO: key nSliceGroups unrecognized, line 11, skipping\n",
      " 1 act-vs-rest.mat\n",
      "nruns = 1\n",
      "autostimdur = \n",
      "\n",
      "\n",
      "outanadir = /data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.rh\n",
      "parfiles condition id list:  1 \n",
      "Found 82503/111586 (73.9) voxels in mask 1\n",
      "Creating Design Matrix\n",
      " ... creation time =  0.002 sec\n",
      "DoMCFit = 1\n",
      "ntptot = 167, nX = 7, DOF = 160\n",
      "Saving X matrix to /data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.rh/Xtmp.mat\n",
      "XCond = 5.86255 (normalized)\n",
      "Computing compensation for resdual AR1 bias\n",
      " 1  -0.5  -0.499416    (t=0.007747)\n",
      " 2  -0.25  -0.262363    (t=0.009384)\n",
      " 3  0  -0.0292773    (t=0.010989)\n",
      " 4  0.25  0.196039    (t=0.012438)\n",
      " 5  0.5  0.403378    (t=0.017)\n",
      "AR1 Correction M: 0.042295 1.10351\n",
      "Computing contrast matrices\n",
      "OLS Beta Pass \n",
      "  run 1    t= 0.0\n",
      "reading data ... 0.655733\n",
      "    Global Mean   825.89\n",
      "Global In-Mask Mean = 825.895 (812.788)\n",
      "Rescale Target = 100\n",
      "RescaleFactor = 0.121081\n",
      "OLS Residual Pass \n",
      "  run 1    t= 0.0\n",
      "reading data ... 0.679765\n",
      "Saving rho1\n",
      "Smoothing ACF\n",
      "/usr/local/freesurfer/bin/mris_fwhm --mask /data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.rh/mask.nii.gz --i /data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.rh/rho1mn.nii.gz --o /data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.rh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s pBrain --hemi rh --sd /usr/local/freesurfer/subjects\n",
      "pBrain rh white\n",
      "Number of vertices 111586\n",
      "Number of faces    223168\n",
      "Total area         73917.976562\n",
      "GroupSurface 0\n",
      "AvgVtxArea       0.662431\n",
      "AvgVtxDist       0.889571\n",
      "StdVtxDist       0.264496\n",
      "Loading mask /data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.rh/mask.nii.gz\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found 82503 voxels in mask\n",
      "Not Polynomial detrending\n",
      "Smoothing input by fwhm=20.000000, gstd=8.493218, niters=223 \n",
      "Only smoothing, so saving and exiting now\n",
      "\n",
      "Found 0 voxels with corrected AR1 > 0.90\n",
      "Whitening\n",
      "Computing whitening matrices\n",
      "Alloc Sinv: 167 167 30 ...  done t = 0.001221 sec\n",
      "  seg   1   2750  nrho1 = 0.076\n",
      "  seg   2   2750  nrho1 = 0.096\n",
      "  seg   3   2750  nrho1 = 0.107\n",
      "  seg   4   2750  nrho1 = 0.115\n",
      "  seg   5   2750  nrho1 = 0.122\n",
      "  seg   6   2750  nrho1 = 0.129\n",
      "  seg   7   2750  nrho1 = 0.134\n",
      "  seg   8   2750  nrho1 = 0.139\n",
      "  seg   9   2750  nrho1 = 0.145\n",
      "  seg  10   2750  nrho1 = 0.150\n",
      "  seg  11   2750  nrho1 = 0.154\n",
      "  seg  12   2750  nrho1 = 0.158\n",
      "  seg  13   2750  nrho1 = 0.162\n",
      "  seg  14   2750  nrho1 = 0.166\n",
      "  seg  15   2750  nrho1 = 0.170\n",
      "  seg  16   2750  nrho1 = 0.173\n",
      "  seg  17   2750  nrho1 = 0.177\n",
      "  seg  18   2750  nrho1 = 0.182\n",
      "  seg  19   2750  nrho1 = 0.187\n",
      "  seg  20   2750  nrho1 = 0.193\n",
      "  seg  21   2750  nrho1 = 0.198\n",
      "  seg  22   2750  nrho1 = 0.203\n",
      "  seg  23   2750  nrho1 = 0.209\n",
      "  seg  24   2750  nrho1 = 0.217\n",
      "  seg  25   2750  nrho1 = 0.227\n",
      "  seg  26   2750  nrho1 = 0.239\n",
      "  seg  27   2750  nrho1 = 0.260\n",
      "  seg  28   2750  nrho1 = 0.286\n",
      "  seg  29   2750  nrho1 = 0.321\n",
      "  seg  30   2753  nrho1 = 0.384\n",
      "GLS Beta Pass \n",
      "  run 1    t= 0.0\n",
      "GLS Residual Pass \n",
      "  run 1    t= 0.0\n",
      "Found 29083 zero-valued voxels\n",
      "Computing contrasts\n",
      "Starting contrasts\n",
      "act-vs-rest J=1 -------------\n",
      "Saving efficiency 31.75\n",
      "Testing Motion Correction Parameters\n",
      " -2.71  -0.92  -3.43  -3.27  -0.14   3.05   1.04   1.30  -0.41  -0.67  -2.77  -0.98   2.33   3.34   1.04   1.30  -1.07  -1.32 \n",
      "Saving h.dat to /data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.rh/h.dat\n",
      "cputime-min 0.057833\n",
      "fast_selxavg3 done for /data/martin/prosopagnosia/landscapes/Sess01\n",
      "\n",
      "ans =\n",
      "\n",
      "     0\n",
      "\n",
      ">> >> >> >> >> ------------------------------------------\n",
      "Started at Fri Nov 24 13:04:51 CET 2017\n",
      "Ended   at Fri Nov 24 13:05:08 CET 2017\n",
      " \n",
      "selxavg3-sess completed\n",
      " \n"
     ]
    }
   ],
   "source": [
    "selxavg3-sess -sf sessids -analysis design.sm5.${hemi}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[34;42m.\u001b[00m\n",
      "├── \u001b[34;42mdesign.sm5.rh\u001b[00m\n",
      "│   ├── \u001b[01;32mact-vs-rest.config\u001b[00m\n",
      "│   ├── \u001b[01;32mact-vs-rest.mat\u001b[00m\n",
      "│   └── \u001b[01;32manalysis.info\u001b[00m\n",
      "├── \u001b[34;42mlog\u001b[00m\n",
      "│   ├── \u001b[01;32mmc-Sess01-bold.log\u001b[00m\n",
      "│   ├── \u001b[01;32mmkbrainmask-Sess01-bold.log\u001b[00m\n",
      "│   ├── \u001b[01;32mmkcontrast-sess.log\u001b[00m\n",
      "│   ├── \u001b[01;32mmktemplate-sess.Sess01.bold.f.log\u001b[00m\n",
      "│   ├── \u001b[01;32mpreproc-Sess01-bold.log\u001b[00m\n",
      "│   ├── \u001b[01;32mpreproc-sess.Sess01.log\u001b[00m\n",
      "│   ├── \u001b[01;32mrawfunc2surf-sess.Sess01.bold.fmcpr.sm5.pBrain.lhrh.log\u001b[00m\n",
      "│   ├── \u001b[01;32mregister-sess.Sess01.log\u001b[00m\n",
      "│   └── \u001b[01;32mselxavg3-sess-bold-design.sm5.rh-171124130451.log\u001b[00m\n",
      "├── \u001b[34;42mSess01\u001b[00m\n",
      "│   ├── \u001b[34;42mbold\u001b[00m\n",
      "│   │   ├── \u001b[34;42m003\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mdesign.par\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mf-infodump.dat\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mfmcpr.mat.aff12.1D\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mfmcpr.mcdat\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mfmcpr.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mfmcpr.nii.gz.mclog\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mfmcpr.sm5.pBrain.lh.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mfmcpr.sm5.pBrain.rh.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mf.nii\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mglobal.meanval.dat\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mglobal.waveform.dat\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32minit.register.dof6.dat\u001b[00m\n",
      "│   │   │   ├── \u001b[34;42mmasks\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mbrain.e3.nii.gz\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mbrain.nii.gz\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mbrain.nii.gz.mkbrainmask.log\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mbrain.pBrain.lh.nii.gz\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mbrain.pBrain.lh.pr.nii.gz\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mbrain.pBrain.rh.nii.gz\u001b[00m\n",
      "│   │   │   │   └── \u001b[01;32mbrain.pBrain.rh.pr.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mmcdat2extreg.log\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mmcprextreg\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mregister.dof6.dat~\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mregister.dof6.dat.log\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mregister.dof6.dat.mincost\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mregister.dof6.dat.param\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mregister.dof6.dat.sum\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mregister.dof6.lta\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mtemplate.log\u001b[00m\n",
      "│   │   │   └── \u001b[01;32mtemplate.nii.gz\u001b[00m\n",
      "│   │   ├── \u001b[34;42mdesign.sm5.rh\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32macfsegLUT.txt\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32macfseg.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[34;42mact-vs-rest\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mces.nii.gz\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mcespct.nii.gz\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mcesvar.nii.gz\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mcesvarpct.nii.gz\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mcnr.nii.gz\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mefficiency.dat\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mF.nii.gz\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mfsig.nii.gz\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mmc.ces.dat\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mmc.minsig.dat\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mmc.sig.dat\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mpcc.nii.gz\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32msig.nii.gz\u001b[00m\n",
      "│   │   │   │   ├── \u001b[01;32mt.nii.gz\u001b[00m\n",
      "│   │   │   │   └── \u001b[01;32mz.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32manalysis.info\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mbeta.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mdof\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mfs.build-stamp.txt\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mfsnr2.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mfsnr.dat\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mfsnr.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mh.dat\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mh.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mh-offset.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mmask.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mmeanfunc.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mnmask.dat\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mnrho1mn.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mraw.fsnr.dat\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mraw.fsnr.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[34;42mres\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mrho1mn.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mrho1mn.sm.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mrho1.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mrstd.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mrvar.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mselxavg3.log\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32msxa3.config.txt\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mX.dat\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mX.mat\u001b[00m\n",
      "│   │   │   └── \u001b[01;32mXtmp.mat\u001b[00m\n",
      "│   │   ├── \u001b[01;32minit.register.dof6.dat\u001b[00m\n",
      "│   │   ├── \u001b[34;42mmasks\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mbrain.e3.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mbrain.nii.gz\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mbrain.nii.gz.mkbrainmask.log\u001b[00m\n",
      "│   │   │   ├── \u001b[01;32mbrain.pBrain.lh.pr.nii.gz\u001b[00m\n",
      "│   │   │   └── \u001b[01;32mbrain.pBrain.rh.pr.nii.gz\u001b[00m\n",
      "│   │   ├── \u001b[01;32mregister.dof6.dat~\u001b[00m\n",
      "│   │   ├── \u001b[01;32mregister.dof6.dat.log\u001b[00m\n",
      "│   │   ├── \u001b[01;32mregister.dof6.dat.mincost\u001b[00m\n",
      "│   │   ├── \u001b[01;32mregister.dof6.dat.param\u001b[00m\n",
      "│   │   ├── \u001b[01;32mregister.dof6.dat.sum\u001b[00m\n",
      "│   │   ├── \u001b[01;32mregister.dof6.lta\u001b[00m\n",
      "│   │   ├── \u001b[01;32mtemplate.log\u001b[00m\n",
      "│   │   └── \u001b[01;32mtemplate.nii.gz\u001b[00m\n",
      "│   ├── \u001b[01;32mdcmunpack.log\u001b[00m\n",
      "│   ├── \u001b[01;32mimagelist.dat\u001b[00m\n",
      "│   ├── \u001b[01;32mseries-info.dat\u001b[00m\n",
      "│   └── \u001b[01;32msubjectname\u001b[00m\n",
      "└── \u001b[01;32msessids\u001b[00m\n",
      "\n",
      "10 directories, 103 files\n"
     ]
    }
   ],
   "source": [
    "tree"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "###  show results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "#tksurfer-sess -s Sess01 -analysis design.sm5.${hemi} -hemi ${hemi} -c act-vs-rest -map t -fthresh 3 -fmax 10"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### do everything for the other hemisphere"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting TER to 0.050000\n",
      "Setting TimeWindow to 40.000000\n",
      "Setting PreStim    to 0\n",
      "Setting PostStim   to 40.000000\n",
      "# FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c\n",
      "# MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $\n",
      "# MKACMD /usr/local/freesurfer/fsfast/bin/mkanalysis-sess -analysis design.sm5.lh -surface pBrain lh -per-run -fwhm 5 -fsd bold -paradigm design.par -event-related -spmhrf 0 -refeventdur 30 -polyfit 2 -mcextreg -nskip 0 -TR 3 -nconditions 1\n",
      "# DATE Fri Nov 24 13:05:09 CET 2017\n",
      "\n",
      "analysis design.sm5.lh\n",
      "mcstem fmcpr\n",
      "fsd bold\n",
      "TR 3\n",
      "RegDOF 6\n",
      "PerSession 0\n",
      "RawSpace surface pBrain lh\n",
      "mask brain\n",
      "RawFWHM 5\n",
      "RawSTC none\n",
      "nSliceGroups 1\n",
      "UseB0DC 0\n",
      "ApplySubCortMask 1\n",
      "inorm 100\n",
      "acfbins 30\n",
      "fixacf  1\n",
      "acffwhm 20\n",
      "acfsvd  0\n",
      "designtype event-related\n",
      "nskip 0\n",
      "polyfit 2\n",
      "HPFCutoffHz 0\n",
      "HeteroGCor 0\n",
      "nconditions 1\n",
      "parname design.par\n",
      "RefEventDur 30\n",
      "timewindow 40.000000\n",
      "prestim 0\n",
      "TER 0.050000\n",
      "spmhrf 0\n",
      "stimulusdelay -1.50000000000000000000\n",
      "Condition 1 Condition01\n",
      "nuisreg mcprextreg 3\n",
      "mkanalysis-sess done\n",
      "INFO: Found 1 Non-Null Conditions\n",
      "INFO: Found 1 Delays\n",
      "Condition Weights: 1.00000000000000000000\n",
      "mkcontrast2 -config design.sm5.lh/act-vs-rest.config -anadir design.sm5.lh -wcond 1.00000000000000000000 -sumconds -o design.sm5.lh/act-vs-rest.mat -wdelay 1 -no-octave\n",
      "  $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $\n",
      "cmtxfile  design.sm5.lh/act-vs-rest.mat\n",
      "nconds    1,  wcond  1.00000000000000000000\n",
      "ndelays   1, wdelay 1\n",
      "ndelays   1, wpsa   \n",
      "sumconds  1\n",
      "sumdelays 0\n",
      "nircorr   0\n",
      "TER       0.050000\n",
      "rdelta    \n",
      "rtau      \n",
      "  cmtxfile  design.sm5.lh/act-vs-rest.mat\n",
      "  monly  0\n",
      "  NCond   1\n",
      "  WCond   1.00000000000000000000\n",
      "  NDelay  1\n",
      "  WDelay  1\n",
      "  TER         0.050000\n",
      "  sumconds   1\n",
      "  sumdelays  0\n",
      "  nircorr  0\n",
      "  TPreStim  0\n",
      "  RmPreStim  0\n",
      "  rdelta     0 0\n",
      "  rtau       0 0\n",
      "  ndelays    1\n",
      "  CNorm      1\n",
      "  setwdelay  0\n",
      "  setwcond   0\n",
      "Matlab file is /tmp/mkcontrast2.25887.m\n",
      "MATLAB is selecting SOFTWARE OPENGL rendering.\n",
      "\n",
      "                            < M A T L A B (R) >\n",
      "                  Copyright 1984-2016 The MathWorks, Inc.\n",
      "                   R2016a (9.0.0.341360) 64-bit (glnxa64)\n",
      "                             February 11, 2016\n",
      "\n",
      " \n",
      "To get started, type one of these: helpwin, helpdesk, or demo.\n",
      "For product information, visit www.mathworks.com.\n",
      " \n",
      "\n",
      "\tThis is a Classroom License for instructional use only.\n",
      "\tResearch and commercial use is prohibited.\n",
      "\n",
      ">> starting mkcontrast2m\n",
      "Normalizing contrast matrix\n",
      "mkcontrast2m done\n",
      ">> Fri Nov 24 13:05:17 CET 2017\n",
      "Surface data pBrain lh\n",
      "--------------------------------------------------------------\n",
      "selxavg3-sess logfile is /data/martin/prosopagnosia/landscapes/log/selxavg3-sess-bold-design.sm5.lh-171124130517.log\n",
      "--------------------------------------------------------------\n",
      "selxavg3-sess log file\n",
      "/usr/local/freesurfer/fsfast/bin/selxavg3-sess\n",
      "-sf sessids -analysis design.sm5.lh\n",
      "$Id: selxavg3-sess,v 1.68 2016/05/10 03:24:18 greve Exp $\n",
      "uid=1000(martin) gid=1000(martin) groups=1000(martin),24(cdrom),25(floppy),29(audio),30(dip),44(video),46(plugdev),108(netdev),110(lpadmin),113(scanner),117(bluetooth),999(docker)\n",
      "/data/martin/prosopagnosia/landscapes\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "Fri Nov 24 13:05:17 CET 2017\n",
      "preproc-sess -s Sess01 -d /data/martin/prosopagnosia/landscapes -a design.sm5.lh -nolog\n",
      "--------------------------------------------------------------\n",
      "preproc-sess logfile is /dev/null\n",
      "--------------------------------------------------------------\n",
      "$Id: preproc-sess,v 1.64.2.1 2016/08/02 21:19:09 greve Exp $\n",
      "martin\n",
      "setenv FREESURFER_HOME /usr/local/freesurfer\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "/data/martin/prosopagnosia/landscapes\n",
      "/usr/local/freesurfer/fsfast/bin/preproc-sess\n",
      "-s Sess01 -d /data/martin/prosopagnosia/landscapes -a design.sm5.lh -nolog\n",
      "Fri Nov 24 13:05:18 CET 2017\n",
      "instem   f \n",
      "mc   1     f fmcpr \n",
      "stc  0     fmcpr\n",
      "sm   0   \n",
      "mask 1   brain\n",
      "Sess01 Template -----------------------------\n",
      "mktemplate-sess -s Sess01 -d /data/martin/prosopagnosia/landscapes -fsd bold -nolog -update\n",
      " \n",
      "Session: /data/martin/prosopagnosia/landscapes/Sess01 ----------------\n",
      "Fri Nov 24 13:05:18 CET 2017\n",
      "Detected input format at nii\n",
      "Sess01 Update not needed\n",
      "  Run: 003 ----------------\n",
      "  Fri Nov 24 13:05:18 CET 2017\n",
      "  Sess01 003 Update not needed\n",
      "Fri Nov 24 13:05:18 CET 2017\n",
      "mktemplate-sess completed \n",
      "Sess01 Registration -----------------------------\n",
      "register-sess -s Sess01 -d /data/martin/prosopagnosia/landscapes -fsd bold -delete-dat -dof 6 -bold -per-run -nolog -update -init-coreg\n",
      "--------------------------------------------------------------\n",
      "register-sess logfile is /dev/null\n",
      "--------------------------------------------------------------\n",
      "Fri Nov 24 13:05:18 CET 2017\n",
      "\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/landscapes\n",
      "/usr/local/freesurfer/fsfast/bin/register-sess -s Sess01 -d /data/martin/prosopagnosia/landscapes -fsd bold -delete-dat -dof 6 -bold -per-run -nolog -update -init-coreg\n",
      "\n",
      "freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      " \n",
      "Session: /data/martin/prosopagnosia/landscapes/Sess01 ----------------\n",
      "Fri Nov 24 13:05:18 CET 2017\n",
      "/data/martin/prosopagnosia/landscapes/Sess01\n",
      "  Run: 003 ----------------\n",
      "Fri Nov 24 13:05:18 CET 2017\n",
      "Update not needed\n",
      "Fri Nov 24 13:05:18 CET 2017\n",
      "register-sess completed \n",
      "Sess01 Mask ------------------------\n",
      "mkbrainmask-sess -maskstem brain -fsd bold -s Sess01 -d /data/martin/prosopagnosia/landscapes -per-run -nolog -update\n",
      "------------------------------------------------\n",
      "/data/martin/prosopagnosia/landscapes/Sess01 \n",
      "Fri Nov 24 13:05:18 CET 2017\n",
      "Sess01 Update not needed for session-level mask\n",
      "Sess01 Update not needed for run 003 mask\n",
      "Sess01 Update not needed for run 003 meanval\n",
      "Fri Nov 24 13:05:18 CET 2017\n",
      "mkbrainmask-sess done\n",
      "Sess01 MC -----------------------------\n",
      "mc-sess -fstem f -fmcstem fmcpr -s Sess01 -d /data/martin/prosopagnosia/landscapes -fsd bold -per-run -nolog -update\n",
      "Logfile is /dev/null\n",
      "-------------------------------------------\n",
      "/data/martin/prosopagnosia/landscapes/Sess01 \n",
      "RunList: 003\n",
      "Sess01 003 Update not needed\n",
      "\n",
      "\n",
      "Fri Nov 24 13:05:18 CET 2017\n",
      "mc-sess completed SUCCESSFULLY\n",
      "Sess01 To Surface -----------------------------\n",
      "rawfunc2surf-sess -fwhm 5 -s Sess01 -d /data/martin/prosopagnosia/landscapes -fsd bold -hemi lh -trgsubject pBrain -nolog -update -per-run\n",
      "instem fmcpr\n",
      "outstem fmcpr.sm5.pBrain.hemi\n",
      "------------------------------ \n",
      "1/1 Sess01\n",
      "  1/1 Sess01 003 lh ---------\n",
      "    Fri Nov 24 13:05:18 CET 2017\n",
      "/data/martin/prosopagnosia/landscapes/Sess01/bold/003/masks/brain.pBrain.lh.pr.nii.gz does not need updating\n",
      "/data/martin/prosopagnosia/landscapes/Sess01/bold/masks/brain.pBrain.lh.pr.nii.gz does not need updating\n",
      "  1/1 Sess01 003 lh ---------\n",
      "    Fri Nov 24 13:05:18 CET 2017\n",
      "    Sess01 003 Update not needed\n",
      "\n",
      "Fri Nov 24 13:05:18 CET 2017\n",
      "rawfunc2surf-sess completed \n",
      "----------------------------------------\n",
      "Started at Fri Nov 24 13:05:18 CET 2017\n",
      "Ended   at Fri Nov 24 13:05:18 CET 2017\n",
      "preproc-sess done\n",
      "-------------------------------------------\n",
      "1/1 /data/martin/prosopagnosia/landscapes/Sess01 \n",
      "Fri Nov 24 13:05:18 CET 2017\n",
      "anadir = /data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.lh\n",
      "DoGLMFit = 1\n",
      "DoContrasts = 1\n",
      "UpdateNeeded = 1\n",
      "    Sess01 Update needed\n",
      "/data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.lh/sxa3.config.txt\n",
      "MLF is /tmp/selxavg3-sess-26172.m\n",
      "------------------------------------------\n",
      "% Fri Nov 24 13:05:18 CET 2017  \n",
      "% /data/martin/prosopagnosia/landscapes  \n",
      "%  design.sm5.lh  \n",
      "which fast_selxavg3\n",
      "which fast_ldanaflac\n",
      "which MRIread\n",
      "  \n",
      "  \n",
      "fast_selxavg3b('/data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.lh/sxa3.config.txt')\n",
      "if(~fast_fileexists('/tmp/selxavg3-sess-26172.ok')); quit; end\n",
      "%--------------------------------\n",
      "  \n",
      "  \n",
      "quit;\n",
      "------------------------------------------\n",
      "------------------------------------------\n",
      "------- matlab output --------------------\n",
      "MATLAB is selecting SOFTWARE OPENGL rendering.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "                            < M A T L A B (R) >\n",
      "                  Copyright 1984-2016 The MathWorks, Inc.\n",
      "                   R2016a (9.0.0.341360) 64-bit (glnxa64)\n",
      "                             February 11, 2016\n",
      "\n",
      " \n",
      "To get started, type one of these: helpwin, helpdesk, or demo.\n",
      "For product information, visit www.mathworks.com.\n",
      " \n",
      "\n",
      "\tThis is a Classroom License for instructional use only.\n",
      "\tResearch and commercial use is prohibited.\n",
      "\n",
      ">> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m\n",
      ">> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m\n",
      ">> /usr/local/freesurfer/matlab/MRIread.m\n",
      ">> >> >> starting fast_selxavg3b\n",
      "\n",
      "\n",
      "#@# Sess01 ###############################\n",
      "/data/martin/prosopagnosia/landscapes/Sess01\n",
      "-------------------------\n",
      "$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $\n",
      "-------------------------\n",
      "outtop = /data/martin/prosopagnosia/landscapes\n",
      "Extension format = nii.gz\n",
      "INFO: key nSliceGroups unrecognized, line 11, skipping\n",
      " 1 act-vs-rest.mat\n",
      "nruns = 1\n",
      "autostimdur = \n",
      "\n",
      "\n",
      "outanadir = /data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.lh\n",
      "parfiles condition id list:  1 \n",
      "Found 83318/112635 (74.0) voxels in mask 1\n",
      "Creating Design Matrix\n",
      " ... creation time =  0.002 sec\n",
      "DoMCFit = 1\n",
      "ntptot = 167, nX = 7, DOF = 160\n",
      "Saving X matrix to /data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.lh/Xtmp.mat\n",
      "XCond = 5.86255 (normalized)\n",
      "Computing compensation for resdual AR1 bias\n",
      " 1  -0.5  -0.499416    (t=0.006673)\n",
      " 2  -0.25  -0.262363    (t=0.008505)\n",
      " 3  0  -0.0292773    (t=0.010285)\n",
      " 4  0.25  0.196039    (t=0.0119)\n",
      " 5  0.5  0.403378    (t=0.016474)\n",
      "AR1 Correction M: 0.042295 1.10351\n",
      "Computing contrast matrices\n",
      "OLS Beta Pass \n",
      "  run 1    t= 0.0\n",
      "reading data ... 0.664561\n",
      "    Global Mean   825.89\n",
      "Global In-Mask Mean = 825.895 (848.906)\n",
      "Rescale Target = 100\n",
      "RescaleFactor = 0.121081\n",
      "OLS Residual Pass \n",
      "  run 1    t= 0.0\n",
      "reading data ... 0.690561\n",
      "Saving rho1\n",
      "Smoothing ACF\n",
      "/usr/local/freesurfer/bin/mris_fwhm --mask /data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.lh/mask.nii.gz --i /data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.lh/rho1mn.nii.gz --o /data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.lh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s pBrain --hemi lh --sd /usr/local/freesurfer/subjects\n",
      "pBrain lh white\n",
      "Number of vertices 112635\n",
      "Number of faces    225266\n",
      "Total area         74093.468750\n",
      "GroupSurface 0\n",
      "AvgVtxArea       0.657819\n",
      "AvgVtxDist       0.887337\n",
      "StdVtxDist       0.259981\n",
      "Loading mask /data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.lh/mask.nii.gz\n",
      "Found 83318 voxels in mask\n",
      "Not Polynomial detrending\n",
      "Smoothing input by fwhm=20.000000, gstd=8.493218, niters=224 \n",
      "Only smoothing, so saving and exiting now\n",
      "\n",
      "Found 0 voxels with corrected AR1 > 0.90\n",
      "Whitening\n",
      "Computing whitening matrices\n",
      "Alloc Sinv: 167 167 30 ...  done t = 0.001329 sec\n",
      "  seg   1   2777  nrho1 = 0.068\n",
      "  seg   2   2777  nrho1 = 0.083\n",
      "  seg   3   2777  nrho1 = 0.095\n",
      "  seg   4   2777  nrho1 = 0.102\n",
      "  seg   5   2777  nrho1 = 0.110\n",
      "  seg   6   2777  nrho1 = 0.117\n",
      "  seg   7   2777  nrho1 = 0.124\n",
      "  seg   8   2777  nrho1 = 0.129\n",
      "  seg   9   2777  nrho1 = 0.135\n",
      "  seg  10   2777  nrho1 = 0.139\n",
      "  seg  11   2777  nrho1 = 0.143\n",
      "  seg  12   2777  nrho1 = 0.147\n",
      "  seg  13   2777  nrho1 = 0.151\n",
      "  seg  14   2777  nrho1 = 0.154\n",
      "  seg  15   2777  nrho1 = 0.159\n",
      "  seg  16   2777  nrho1 = 0.163\n",
      "  seg  17   2777  nrho1 = 0.168\n",
      "  seg  18   2777  nrho1 = 0.173\n",
      "  seg  19   2777  nrho1 = 0.179\n",
      "  seg  20   2777  nrho1 = 0.184\n",
      "  seg  21   2777  nrho1 = 0.191\n",
      "  seg  22   2777  nrho1 = 0.198\n",
      "  seg  23   2777  nrho1 = 0.206\n",
      "  seg  24   2777  nrho1 = 0.214\n",
      "  seg  25   2777  nrho1 = 0.222\n",
      "  seg  26   2777  nrho1 = 0.231\n",
      "  seg  27   2777  nrho1 = 0.247\n",
      "  seg  28   2777  nrho1 = 0.268\n",
      "  seg  29   2777  nrho1 = 0.296\n",
      "  seg  30   2785  nrho1 = 0.332\n",
      "GLS Beta Pass \n",
      "  run 1    t= 0.0\n",
      "GLS Residual Pass \n",
      "  run 1    t= 0.0\n",
      "Found 29317 zero-valued voxels\n",
      "Computing contrasts\n",
      "Starting contrasts\n",
      "act-vs-rest J=1 -------------\n",
      "Saving efficiency 31.75\n",
      "Testing Motion Correction Parameters\n",
      " -2.71  -0.92  -3.43  -3.27  -0.14   3.05   1.04   1.30  -0.41  -0.67  -2.77  -0.98   2.33   3.34   1.04   1.30  -1.07  -1.32 \n",
      "Saving h.dat to /data/martin/prosopagnosia/landscapes/Sess01/bold/design.sm5.lh/h.dat\n",
      "cputime-min 0.058000\n",
      "fast_selxavg3 done for /data/martin/prosopagnosia/landscapes/Sess01\n",
      "\n",
      "ans =\n",
      "\n",
      "     0\n",
      "\n",
      ">> >> >> >> >> ------------------------------------------\n",
      "Started at Fri Nov 24 13:05:17 CET 2017\n",
      "Ended   at Fri Nov 24 13:05:34 CET 2017\n",
      " \n",
      "selxavg3-sess completed\n",
      " \n"
     ]
    }
   ],
   "source": [
    "hemi=\"lh\"\n",
    "\n",
    "mkanalysis-sess -analysis design.sm5.${hemi} \\\n",
    "-surface pBrain ${hemi} \\\n",
    "-per-run \\\n",
    "-fwhm 5 \\\n",
    "-fsd bold \\\n",
    "-paradigm design.par \\\n",
    "-event-related \\\n",
    "-spmhrf 0 \\\n",
    "-refeventdur 30 \\\n",
    "-polyfit 2 \\\n",
    "-mcextreg \\\n",
    "-nskip 0 \\\n",
    "-TR 3 \\\n",
    "-nconditions 1\n",
    "\n",
    "mkcontrast-sess -analysis design.sm5.${hemi} -contrast act-vs-rest -a 1 -c 0\n",
    "\n",
    "selxavg3-sess -sf sessids -analysis design.sm5.${hemi}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "#tksurfer-sess -s Sess01 -analysis design.sm5.${hemi} -hemi ${hemi} -c act-vs-rest -map t -fthresh 3 -fmax 10"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### do everything for the other paradigm"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "Change into experiment directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "cd ${projectDir}hands"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[34;42m.\u001b[00m\n",
      "└── \u001b[34;42mSess01\u001b[00m\n",
      "    ├── \u001b[34;42mbold\u001b[00m\n",
      "    │   └── \u001b[34;42m005\u001b[00m\n",
      "    │       ├── \u001b[01;32mf-infodump.dat\u001b[00m\n",
      "    │       └── \u001b[01;32mf.nii\u001b[00m\n",
      "    ├── \u001b[01;32mdcmunpack.log\u001b[00m\n",
      "    ├── \u001b[01;32mimagelist.dat\u001b[00m\n",
      "    └── \u001b[01;32mseries-info.dat\u001b[00m\n",
      "\n",
      "3 directories, 5 files\n"
     ]
    }
   ],
   "source": [
    "tree"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "add meta-info"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[34;42m.\u001b[00m\n",
      "├── \u001b[34;42mSess01\u001b[00m\n",
      "│   ├── \u001b[34;42mbold\u001b[00m\n",
      "│   │   └── \u001b[34;42m005\u001b[00m\n",
      "│   │       ├── \u001b[01;32mf-infodump.dat\u001b[00m\n",
      "│   │       └── \u001b[01;32mf.nii\u001b[00m\n",
      "│   ├── \u001b[01;32mdcmunpack.log\u001b[00m\n",
      "│   ├── \u001b[01;32mimagelist.dat\u001b[00m\n",
      "│   ├── \u001b[01;32mseries-info.dat\u001b[00m\n",
      "│   └── \u001b[01;32msubjectname\u001b[00m\n",
      "└── \u001b[01;32msessids\u001b[00m\n",
      "\n",
      "3 directories, 7 files\n"
     ]
    }
   ],
   "source": [
    "echo Sess01 > ${projectDir}hands/sessids\n",
    "echo pBrain >  ${projectDir}hands/Sess01/subjectname\n",
    "\n",
    "tree"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "add design file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\t1\t12\t1\tface\n",
      "12\t0\t12\t1\thand\n",
      "24\t1\t12\t1\tface\n",
      "36\t0\t12\t1\thand\n",
      "48\t1\t12\t1\tface\n",
      "60\t0\t12\t1\thand\n",
      "72\t1\t12\t1\tface\n",
      "84\t0\t12\t1\thand\n",
      "96\t1\t12\t1\tface\n",
      "108\t0\t12\t1\thand\n",
      "120\t1\t12\t1\tface\n",
      "132\t0\t12\t1\thand\n",
      "144\t1\t12\t1\tface\n",
      "156\t0\t12\t1\thand\n",
      "168\t1\t12\t1\tface\n",
      "180\t0\t12\t1\thand\n",
      "192\t1\t12\t1\tface\n",
      "204\t0\t12\t1\thand\n",
      "216\t1\t12\t1\tface\n",
      "228\t0\t12\t1\thand\n",
      "240\t1\t12\t1\tface\n",
      "252\t0\t12\t1\thand\n",
      "264\t1\t12\t1\tface\n",
      "276\t0\t12\t1\thand\n",
      "288\t1\t12\t1\tface\n",
      "300\t0\t12\t1\thand\n",
      "312\t1\t12\t1\tface\n",
      "324\t0\t12\t1\thand\n",
      "336\t1\t12\t1\tface\n",
      "348\t0\t12\t1\thand\n",
      "360\t1\t12\t1\tface\n",
      "372\t0\t12\t1\thand\n",
      "384\t1\t12\t1\tface\n",
      "396\t0\t12\t1\thand\n",
      "408\t1\t12\t1\tface\n",
      "420\t0\t12\t1\thand\n",
      "432\t1\t12\t1\tface\n",
      "444\t0\t12\t1\thand\n",
      "456\t1\t12\t1\tface\n",
      "468\t0\t12\t1\thand\n",
      "480\t1\t12\t1\tface\n",
      "492\t0\t12\t1\thand\n",
      "504\t1\t12\t1\tface\n",
      "516\t0\t12\t1\thand\n",
      "528\t1\t12\t1\tface\n",
      "540\t0\t12\t1\thand\n",
      "552\t1\t12\t1\tface\n",
      "564\t0\t12\t1\thand\n"
     ]
    }
   ],
   "source": [
    "cp ${projectDir}design/handDesign.par ./Sess01/bold/005/design.par\n",
    "cat Sess01/bold/005/design.par"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "preprocess"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--------------------------------------------------------------\n",
      "preproc-sess logfile is log/preproc-sess.Sess01.log\n",
      "--------------------------------------------------------------\n",
      "$Id: preproc-sess,v 1.64.2.1 2016/08/02 21:19:09 greve Exp $\n",
      "martin\n",
      "setenv FREESURFER_HOME /usr/local/freesurfer\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "/data/martin/prosopagnosia/hands\n",
      "/usr/local/freesurfer/fsfast/bin/preproc-sess\n",
      "-sf sessids -surface pBrain lhrh -fwhm 5 -per-run -fsd bold\n",
      "Fri Nov 24 13:05:35 CET 2017\n",
      "instem   f \n",
      "mc   1     f fmcpr \n",
      "stc  0     fmcpr\n",
      "sm   0   \n",
      "mask 1   brain\n",
      "Sess01 Template -----------------------------\n",
      "mktemplate-sess -s Sess01 -d /data/martin/prosopagnosia/hands -fsd bold -update\n",
      " \n",
      "Session: /data/martin/prosopagnosia/hands/Sess01 ----------------\n",
      "Fri Nov 24 13:05:35 CET 2017\n",
      "Detected input format at nii\n",
      "/data/martin/prosopagnosia/hands\n",
      "mri_convert /data/martin/prosopagnosia/hands/Sess01/bold/005/f.nii /data/martin/prosopagnosia/hands/Sess01/bold/template.nii.gz --frame 0\n",
      "mri_convert.bin /data/martin/prosopagnosia/hands/Sess01/bold/005/f.nii /data/martin/prosopagnosia/hands/Sess01/bold/template.nii.gz --frame 0 \n",
      "$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $\n",
      "reading from /data/martin/prosopagnosia/hands/Sess01/bold/005/f.nii...\n",
      "TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00\n",
      "i_ras = (-0.999463, -0.0273032, 0.0181267)\n",
      "j_ras = (0.022681, -0.975511, -0.21878)\n",
      "k_ras = (0.0236561, -0.218251, 0.975606)\n",
      "keeping frame 0\n",
      "writing to /data/martin/prosopagnosia/hands/Sess01/bold/template.nii.gz...\n",
      "  Run: 005 ----------------\n",
      "  Fri Nov 24 13:05:45 CET 2017\n",
      "/data/martin/prosopagnosia/hands\n",
      "mri_convert /data/martin/prosopagnosia/hands/Sess01/bold/005/f.nii /data/martin/prosopagnosia/hands/Sess01/bold/005/template.nii.gz --mid-frame\n",
      "mri_convert.bin /data/martin/prosopagnosia/hands/Sess01/bold/005/f.nii /data/martin/prosopagnosia/hands/Sess01/bold/005/template.nii.gz --mid-frame \n",
      "$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $\n",
      "reading from /data/martin/prosopagnosia/hands/Sess01/bold/005/f.nii...\n",
      "TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00\n",
      "i_ras = (-0.999463, -0.0273032, 0.0181267)\n",
      "j_ras = (0.022681, -0.975511, -0.21878)\n",
      "k_ras = (0.0236561, -0.218251, 0.975606)\n",
      "keeping frame 98\n",
      "writing to /data/martin/prosopagnosia/hands/Sess01/bold/005/template.nii.gz...\n",
      "Fri Nov 24 13:05:54 CET 2017\n",
      "mktemplate-sess completed \n",
      "Sess01 Registration -----------------------------\n",
      "register-sess -s Sess01 -d /data/martin/prosopagnosia/hands -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg\n",
      "--------------------------------------------------------------\n",
      "register-sess logfile is /data/martin/prosopagnosia/hands/log/register-sess.Sess01.log\n",
      "--------------------------------------------------------------\n",
      "Fri Nov 24 13:05:54 CET 2017\n",
      "\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/hands\n",
      "/usr/local/freesurfer/fsfast/bin/register-sess -s Sess01 -d /data/martin/prosopagnosia/hands -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg\n",
      "\n",
      "freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      " \n",
      "Session: /data/martin/prosopagnosia/hands/Sess01 ----------------\n",
      "Fri Nov 24 13:05:54 CET 2017\n",
      "--------------------------------------\n",
      "/data/martin/prosopagnosia/hands/Sess01\n",
      "bbregister --s pBrain --init-coreg --6 --bold --mov bold/template.nii.gz --reg bold/register.dof6.dat --lta bold/register.dof6.lta --init-reg-out bold/init.register.dof6.dat\n",
      "tmp bold/tmp.bbregister.27486\n",
      "Log file is bold/register.dof6.dat.log\n",
      "Fri Nov 24 13:05:54 CET 2017\n",
      "\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/hands/Sess01\n",
      "/usr/local/freesurfer/bin/bbregister --s pBrain --init-coreg --6 --bold --mov bold/template.nii.gz --reg bold/register.dof6.dat --lta bold/register.dof6.lta --init-reg-out bold/init.register.dof6.dat\n",
      "\n",
      "$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "FREESURFER_HOME /usr/local/freesurfer\n",
      "mri_convert bold/template.nii.gz bold/tmp.bbregister.27486/template.nii\n",
      "mri_convert.bin bold/template.nii.gz bold/tmp.bbregister.27486/template.nii \n",
      "$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $\n",
      "reading from bold/template.nii.gz...\n",
      "TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00\n",
      "i_ras = (-0.999463, -0.0273032, 0.0181267)\n",
      "j_ras = (0.022681, -0.975511, -0.21878)\n",
      "k_ras = (0.0236561, -0.218251, 0.975606)\n",
      "writing to bold/tmp.bbregister.27486/template.nii...\n",
      "mri_coreg --s pBrain --mov bold/tmp.bbregister.27486/template.nii --regdat bold/tmp.bbregister.27486/reg.init.dat --reg bold/tmp.bbregister.27486/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01\n",
      "\n",
      "$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/hands/Sess01\n",
      "cmdline mri_coreg --s pBrain --mov bold/tmp.bbregister.27486/template.nii --regdat bold/tmp.bbregister.27486/reg.init.dat --reg bold/tmp.bbregister.27486/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "dof    6\n",
      "nsep    1\n",
      "cras0    1\n",
      "ftol    0.000100\n",
      "linmintol    0.010000\n",
      "bf       1\n",
      "bflim    30.000000\n",
      "bfnsamp    30\n",
      "SmoothRef 0\n",
      "SatPct    99.990000\n",
      "MovOOB 0\n",
      "optschema 1\n",
      "Reading in mov bold/tmp.bbregister.27486/template.nii\n",
      "Reading in ref /usr/local/freesurfer/subjects/pBrain/mri/brainmask.mgz\n",
      "Reading in and applying refmask /usr/local/freesurfer/subjects/pBrain/mri/aparc+aseg.mgz\n",
      "Setting cras translation parameters to align centers\n",
      "Creating random numbers for coordinate dithering\n",
      "Performing intensity dithering\n",
      "Initial parameters  4.8266 -14.2690  7.8386  0.0000  0.0000  0.0000  1.0000  1.0000  1.0000  0.0000  0.0000  0.0000 \n",
      "Separation list (1):  4   min = 4\n",
      "DoSmoothing 1\n",
      "DoCoordDither 1\n",
      "DoIntensityDither 1\n",
      "nitersmax 4\n",
      "ftol 1.000e-04\n",
      "linmintol 1.000e-02\n",
      "SatPct 99.990000\n",
      "Hist FWHM 7.000000 7.000000\n",
      "nthreads 1\n",
      "movsat = 1629.0000\n",
      "mov gstd 1.6917 1.6917 1.6917\n",
      "Smoothing mov\n",
      "refsat = 115.0000\n",
      "ref gstd 1.8914 1.8914 1.8914\n",
      "Smoothing ref\n",
      "COREGpreproc() done\n",
      "Testing if mov and target overlap\n",
      "Init cost   -1.0424056042\n",
      "nhits = 78038 out of 16777216, Percent Overlap:  29.8\n",
      "Initial  RefRAS-to-MovRAS\n",
      " 1.00000   0.00000   0.00000   4.82664;\n",
      " 0.00000   1.00000   0.00000  -14.26899;\n",
      " 0.00000   0.00000   1.00000   7.83862;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Initial  RefVox-to-MovVox\n",
      " 0.49973  -0.00906  -0.01365   2.68039;\n",
      "-0.01134   0.10939  -0.48776   113.18749;\n",
      "-0.01183  -0.48780  -0.10913   97.11647;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "sep = 4 -----------------------------------\n",
      "COREGoptBruteForce() 30 1 30\n",
      "Turning on MovOOB for BruteForce Search\n",
      "#BF# sep= 4 iter=0 lim=30.0 delta=2.00   4.82664  -0.26899 -10.16138   2.00000   2.00000   0.00000   -1.0314137\n",
      "Turning  MovOOB back off after brute force search\n",
      "\n",
      "\n",
      "---------------------------------\n",
      "Init Powel Params dof = 6\n",
      "Starting OpenPowel2(), sep = 4\n",
      "InitialCost        -1.0696687698 \n",
      "#@#  4  188  4.82664 -0.26899 -10.16138 2.00000 2.00000 0.00000   -1.0696688\n",
      "fs_powell::minimize\n",
      "  nparams 6\n",
      "  maxfev 4\n",
      "  ftol   0.000100\n",
      "  linmin_xtol_   0.010000\n",
      "  powell nthiter 0: fret = -1.069669\n",
      "#@#  4  195  4.74560 -0.26899 -10.16138 2.00000 2.00000 0.00000   -1.0696708\n",
      "#@#  4  199  4.71712 -0.26899 -10.16138 2.00000 2.00000 0.00000   -1.0696716\n",
      "#@#  4  200  4.69807 -0.26899 -10.16138 2.00000 2.00000 0.00000   -1.0696723\n",
      "#@#  4  204  4.69807 -1.88702 -10.16138 2.00000 2.00000 0.00000   -1.0719180\n",
      "#@#  4  207  4.69807 -5.90455 -10.16138 2.00000 2.00000 0.00000   -1.0723306\n",
      "#@#  4  209  4.69807 -4.07598 -10.16138 2.00000 2.00000 0.00000   -1.0734576\n",
      "#@#  4  213  4.69807 -4.09664 -10.16138 2.00000 2.00000 0.00000   -1.0734603\n",
      "#@#  4  217  4.69807 -4.09664 -9.16138 2.00000 2.00000 0.00000   -1.0742857\n",
      "#@#  4  220  4.69807 -4.09664 -8.54335 2.00000 2.00000 0.00000   -1.0744773\n",
      "#@#  4  222  4.69807 -4.09664 -8.46836 2.00000 2.00000 0.00000   -1.0744867\n",
      "#@#  4  230  4.69807 -4.09664 -8.46836 1.38197 2.00000 0.00000   -1.0744947\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "#@#  4  232  4.69807 -4.09664 -8.46836 1.66559 2.00000 0.00000   -1.0745091\n",
      "#@#  4  233  4.69807 -4.09664 -8.46836 1.65559 2.00000 0.00000   -1.0745175\n",
      "#@#  4  234  4.69807 -4.09664 -8.46836 1.53164 2.00000 0.00000   -1.0745311\n",
      "#@#  4  238  4.69807 -4.09664 -8.46836 1.54164 2.00000 0.00000   -1.0745358\n",
      "#@#  4  244  4.69807 -4.09664 -8.46836 1.54164 1.38197 0.00000   -1.0746105\n",
      "#@#  4  248  4.69807 -4.09664 -8.46836 1.54164 1.35483 0.00000   -1.0746125\n",
      "#@#  4  250  4.69807 -4.09664 -8.46836 1.54164 1.36483 0.00000   -1.0746140\n",
      "#@#  4  256  4.69807 -4.09664 -8.46836 1.54164 1.36483 0.38197   -1.0746628\n",
      "#@#  4  261  4.69807 -4.09664 -8.46836 1.54164 1.36483 0.39197   -1.0746644\n",
      "  powell nthiter 1: fret = -1.074664\n",
      "#@#  4  269  5.08004 -4.09664 -8.46836 1.54164 1.36483 0.39197   -1.0747558\n",
      "#@#  4  272  5.14860 -4.09664 -8.46836 1.54164 1.36483 0.39197   -1.0747567\n",
      "#@#  4  273  5.11951 -4.09664 -8.46836 1.54164 1.36483 0.39197   -1.0747582\n",
      "#@#  4  282  5.11951 -4.12269 -8.46836 1.54164 1.36483 0.39197   -1.0747585\n",
      "#@#  4  284  5.11951 -4.11269 -8.46836 1.54164 1.36483 0.39197   -1.0747589\n",
      "#@#  4  291  5.11951 -4.11269 -8.31583 1.54164 1.36483 0.39197   -1.0747772\n",
      "#@#  4  301  5.11951 -4.11269 -8.31583 1.53164 1.36483 0.39197   -1.0747774\n",
      "#@#  4  302  5.11951 -4.11269 -8.31583 1.51589 1.36483 0.39197   -1.0747794\n",
      "#@#  4  313  5.11951 -4.11269 -8.31583 1.51589 1.10032 0.39197   -1.0747842\n",
      "#@#  4  323  5.11951 -4.11269 -8.31583 1.51589 1.11032 0.77393   -1.0748698\n",
      "#@#  4  325  5.11951 -4.11269 -8.31583 1.51589 1.11032 0.78393   -1.0748699\n",
      "#@#  4  326  5.11951 -4.11269 -8.31583 1.51589 1.11032 0.79393   -1.0748705\n",
      "#@#  4  330  5.54094 -4.12873 -8.16330 1.49014 0.85582 1.19590   -1.0749630\n",
      "#@#  4  337  5.59646 -4.13084 -8.14321 1.48675 0.82229 1.24885   -1.0749724\n",
      "  powell nthiter 2: fret = -1.074972\n",
      "#@#  4  365  5.59646 -4.12084 -8.14321 1.48675 0.82229 1.24885   -1.0749725\n",
      "#@#  4  366  5.59646 -4.10773 -8.14321 1.48675 0.82229 1.24885   -1.0749736\n",
      "#@#  4  377  5.59646 -4.10773 -8.08748 1.48675 0.82229 1.24885   -1.0749749\n",
      "#@#  4  381  5.59646 -4.10773 -8.09748 1.48675 0.82229 1.24885   -1.0749772\n",
      "#@#  4  391  5.59646 -4.10773 -8.09748 1.50162 0.82229 1.24885   -1.0749819\n",
      "Powell done niters total = 2\n",
      "OptTimeSec  8.6 sec\n",
      "OptTimeMin  0.14 min\n",
      "nEvals 415\n",
      "Final parameters   5.59646034  -4.10772753  -8.09748173   1.50162423   0.82229155   1.24884915 \n",
      "Final cost   -1.074981917165466\n",
      " \n",
      "\n",
      "---------------------------------\n",
      "mri_coreg utimesec    46.336000\n",
      "mri_coreg stimesec    0.128000\n",
      "mri_coreg ru_maxrss   427084\n",
      "mri_coreg ru_ixrss    0\n",
      "mri_coreg ru_idrss    0\n",
      "mri_coreg ru_isrss    0\n",
      "mri_coreg ru_minflt   126904\n",
      "mri_coreg ru_majflt   0\n",
      "mri_coreg ru_nswap    0\n",
      "mri_coreg ru_inblock  0\n",
      "mri_coreg ru_oublock  0\n",
      "mri_coreg ru_msgsnd   0\n",
      "mri_coreg ru_msgrcv   0\n",
      "mri_coreg ru_nsignals 0\n",
      "mri_coreg ru_nvcsw    46\n",
      "mri_coreg ru_nivcsw   84\n",
      "Final  RefRAS-to-MovRAS\n",
      " 0.99966   0.02179   0.01435   5.59646;\n",
      "-0.02216   0.99941   0.02620  -4.10773;\n",
      "-0.01377  -0.02651   0.99955  -8.09748;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Final  RefVox-to-MovVox\n",
      " 0.49938  -0.00153  -0.02477   2.63768;\n",
      "-0.02365   0.12196  -0.48432   109.67152;\n",
      "-0.00752  -0.48490  -0.12174   88.99670;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Final parameters  5.5965 -4.1077 -8.0975  1.5016  0.8223  1.2488 \n",
      "nhits = 76021 out of 16777216, Percent Overlap:  29.0\n",
      "mri_coreg RunTimeSec 46.5 sec\n",
      "To check run:\n",
      "   tkregisterfv --mov bold/tmp.bbregister.27486/template.nii --targ /usr/local/freesurfer/subjects/pBrain/mri/brainmask.mgz --reg bold/tmp.bbregister.27486/mri_coreg.lta --s pBrain --surfs \n",
      "\n",
      "mri_coreg done\n",
      "\n",
      "mri_segreg --mov bold/tmp.bbregister.27486/template.nii --init-reg bold/tmp.bbregister.27486/reg.init.dat --out-reg bold/tmp.bbregister.27486/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5\n",
      "$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/hands/Sess01\n",
      "mri_segreg --mov bold/tmp.bbregister.27486/template.nii --init-reg bold/tmp.bbregister.27486/reg.init.dat --out-reg bold/tmp.bbregister.27486/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "movvol bold/tmp.bbregister.27486/template.nii\n",
      "regfile bold/tmp.bbregister.27486/reg.init.dat\n",
      "subject pBrain\n",
      "dof 6\n",
      "outregfile bold/tmp.bbregister.27486/bbr.pass1.dat\n",
      "UseMask 0\n",
      "UseLH 1\n",
      "UseRH 1\n",
      "nsubsamp 100\n",
      "PenaltySign  -1\n",
      "PenaltySlope 0.500000\n",
      "PenaltyCenter 0.000000\n",
      "surfname white\n",
      "GMProjFrac 0.500000\n",
      "WMProjAbs 2.000000\n",
      "lhcostfile (null)\n",
      "rhcostfile (null)\n",
      "interp  trilinear (1)\n",
      "frame  0\n",
      "TolPowell 0.000100\n",
      "nMaxItersPowell 36\n",
      "n1dmin  3\n",
      "Profile   0\n",
      "Gdiag_no  -1\n",
      "AddNoise  0 (0)\n",
      "SynthSeed 1512263486\n",
      "TransRandMax 0.000000\n",
      "RotRandMax 0.000000\n",
      "Translations 0.000000 0.000000 0.000000\n",
      "Rotations   0.000000 0.000000 0.000000\n",
      "Input reg\n",
      " 0.99877   0.04955  -0.00306   1.61636;\n",
      " 0.01505  -0.24347   0.96979  -19.23062;\n",
      "-0.04731   0.96864   0.24392   7.47685;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Loading mov\n",
      "Projecting LH Surfs\n",
      "Loading lh.white surf\n",
      "Loading lh.thickness for GM\n",
      "GM Proj: 1 0.500000 2.000000\n",
      "WM Proj: 0 0.500000 2.000000\n",
      "Projecting RH Surfs\n",
      "Loading rh.white surf\n",
      "Loading rh.thickness for GM\n",
      "Projecting RH Surfs\n",
      "Using lh.cortex.label\n",
      "Using rh.cortex.label\n",
      "Computing relative cost\n",
      " 0  -25.0 -25.0 -25.0   0.980071\n",
      " 1  -25.0 -25.0  25.0   1.022608\n",
      " 2  -25.0  25.0 -25.0   0.999352\n",
      " 3  -25.0  25.0  25.0   1.020238\n",
      " 4   25.0 -25.0 -25.0   1.036120\n",
      " 5   25.0 -25.0  25.0   1.023893\n",
      " 6   25.0  25.0 -25.0   1.049420\n",
      " 7   25.0  25.0  25.0   1.052469\n",
      "REL:  8  0.594036    8.184172  1.023021 rel = 0.580669 \n",
      "Initial costs ----------------\n",
      "Number of surface hits 1608\n",
      "WM  Intensity   769.1031 +/- 105.7386\n",
      "Ctx Intensity   815.0839 +/- 151.6264\n",
      "Pct Contrast      4.4753 +/-  21.3234\n",
      "Cost   0.5940\n",
      "RelCost   0.5807\n",
      "\n",
      "------------------------------------\n",
      "Brute force preopt -4 4 4, n = 729\n",
      "     0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      1.0836   1.0836  0.0\n",
      "     1  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   0.0000      1.0685   1.0685  0.0\n",
      "     2  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   4.0000      1.0597   1.0597  0.0\n",
      "     3  -4.0000  -4.0000  -4.0000  -4.0000   0.0000  -4.0000      1.0522   1.0522  0.0\n",
      "     4  -4.0000  -4.0000  -4.0000  -4.0000   0.0000   0.0000      1.0390   1.0390  0.0\n",
      "     5  -4.0000  -4.0000  -4.0000  -4.0000   0.0000   4.0000      1.0373   1.0373  0.0\n",
      "     6  -4.0000  -4.0000  -4.0000  -4.0000   4.0000  -4.0000      0.9492   0.9492  0.0\n",
      "    15  -4.0000  -4.0000  -4.0000   0.0000   4.0000  -4.0000      0.9279   0.9279  0.0\n",
      "    34  -4.0000  -4.0000   0.0000  -4.0000   4.0000   0.0000      0.9224   0.9224  0.0\n",
      "    45  -4.0000  -4.0000   0.0000   4.0000  -4.0000  -4.0000      0.8926   0.8926  0.0\n",
      "   106  -4.0000   0.0000  -4.0000   4.0000   4.0000   0.0000      0.8686   0.8686  0.0\n",
      "   118  -4.0000   0.0000   0.0000   0.0000  -4.0000   0.0000      0.8447   0.8447  0.0\n",
      "   265   0.0000  -4.0000  -4.0000   4.0000   0.0000   0.0000      0.8299   0.8299  0.0\n",
      "   292   0.0000  -4.0000   0.0000   4.0000   0.0000   0.0000      0.7683   0.7683  0.0\n",
      "   337   0.0000   0.0000  -4.0000   0.0000   0.0000   0.0000      0.7149   0.7149  0.0\n",
      "   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.5940   0.5940  0.0\n",
      "Brute Force --------------------------\n",
      "Min cost was 0.594036\n",
      "Number of iterations   729\n",
      "Search time 0.616000 sec\n",
      "Parameters at best (transmm, rotdeg)\n",
      "  0.000   0.000   0.000  0.000  0.000  0.000 \n",
      "--------------------------------------------\n",
      "\n",
      "Starting Powell Minimization\n",
      "Init Powel Params dof = 6\n",
      "0 0\n",
      "1 0\n",
      "2 0\n",
      "3 0\n",
      "4 0\n",
      "5 0\n",
      "fs_powell::minimize\n",
      "  nparams 6\n",
      "  maxfev 36\n",
      "  ftol   0.000100\n",
      "  linmin_xtol_   0.001000\n",
      "  powell nthiter 0: fret = 0.594036\n",
      "   6  0.382  0.000  0.000  0.000  0.000  0.000   0.5867514351\n",
      "   9  0.415  0.000  0.000  0.000  0.000  0.000   0.5864169090\n",
      "  11  0.445  0.000  0.000  0.000  0.000  0.000   0.5863662978\n",
      "  12  0.436  0.000  0.000  0.000  0.000  0.000   0.5863504562\n",
      "  13  0.435  0.000  0.000  0.000  0.000  0.000   0.5863502797\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "  19  0.435 -0.618  0.000  0.000  0.000  0.000   0.5671370309\n",
      "  21  0.435 -0.643  0.000  0.000  0.000  0.000   0.5670346911\n",
      "  23  0.435 -0.640  0.000  0.000  0.000  0.000   0.5669702938\n",
      "  30  0.435 -0.640 -1.618  0.000  0.000  0.000   0.4990531447\n",
      "  36  0.435 -0.640 -1.624  0.000  0.000  0.000   0.4989635558\n",
      "  38  0.435 -0.640 -1.708  0.000  0.000  0.000   0.4985683603\n",
      "  39  0.435 -0.640 -1.684  0.000  0.000  0.000   0.4984693340\n",
      "  41  0.435 -0.640 -1.685  0.000  0.000  0.000   0.4984691822\n",
      "  44  0.435 -0.640 -1.685  1.000  0.000  0.000   0.4758143597\n",
      "  48  0.435 -0.640 -1.685  0.618  0.000  0.000   0.4705602281\n",
      "  49  0.435 -0.640 -1.685  0.577  0.000  0.000   0.4704634767\n",
      "  51  0.435 -0.640 -1.685  0.575  0.000  0.000   0.4704584325\n",
      "  52  0.435 -0.640 -1.685  0.569  0.000  0.000   0.4704501887\n",
      "  59  0.435 -0.640 -1.685  0.569 -0.618  0.000   0.4697255138\n",
      "  61  0.435 -0.640 -1.685  0.569 -0.320  0.000   0.4614820225\n",
      "  62  0.435 -0.640 -1.685  0.569 -0.316  0.000   0.4614752839\n",
      "  63  0.435 -0.640 -1.685  0.569 -0.310  0.000   0.4614727145\n",
      "  71  0.435 -0.640 -1.685  0.569 -0.310  0.382   0.4560956566\n",
      "  77  0.435 -0.640 -1.685  0.569 -0.310  0.379   0.4560891269\n",
      "  powell nthiter 1: fret = 0.456089\n",
      "  87  0.239 -0.640 -1.685  0.569 -0.310  0.379   0.4537294912\n",
      "  88  0.265 -0.640 -1.685  0.569 -0.310  0.379   0.4534752402\n",
      "  89  0.290 -0.640 -1.685  0.569 -0.310  0.379   0.4534625455\n",
      "  90  0.279 -0.640 -1.685  0.569 -0.310  0.379   0.4534300025\n",
      "  91  0.278 -0.640 -1.685  0.569 -0.310  0.379   0.4534284008\n",
      " 100  0.278 -0.852 -1.685  0.569 -0.310  0.379   0.4462463831\n",
      " 102  0.278 -0.847 -1.685  0.569 -0.310  0.379   0.4461812757\n",
      " 105  0.278 -0.836 -1.685  0.569 -0.310  0.379   0.4460469695\n",
      " 108  0.278 -0.833 -1.685  0.569 -0.310  0.379   0.4460153491\n",
      " 109  0.278 -0.831 -1.685  0.569 -0.310  0.379   0.4459955967\n",
      " 119  0.278 -0.831 -1.682  0.569 -0.310  0.379   0.4459932585\n",
      " 127  0.278 -0.831 -1.682  0.951 -0.310  0.379   0.4458621810\n",
      " 129  0.278 -0.831 -1.682  1.187 -0.310  0.379   0.4431696376\n",
      " 132  0.278 -0.831 -1.682  1.174 -0.310  0.379   0.4431601246\n",
      " 135  0.278 -0.831 -1.682  1.173 -0.310  0.379   0.4431598841\n",
      " 136  0.278 -0.831 -1.682  1.172 -0.310  0.379   0.4431598425\n",
      " 141  0.278 -0.831 -1.682  1.172 -0.928  0.379   0.4427311422\n",
      " 143  0.278 -0.831 -1.682  1.172 -0.623  0.379   0.4339281923\n",
      " 146  0.278 -0.831 -1.682  1.172 -0.577  0.379   0.4335198516\n",
      " 147  0.278 -0.831 -1.682  1.172 -0.591  0.379   0.4334179015\n",
      " 150  0.278 -0.831 -1.682  1.172 -0.597  0.379   0.4334118144\n",
      " 151  0.278 -0.831 -1.682  1.172 -0.595  0.379   0.4334112635\n",
      " 159  0.278 -0.831 -1.682  1.172 -0.595  0.114   0.4313924376\n",
      " 160  0.278 -0.831 -1.682  1.172 -0.595  0.146   0.4308273042\n",
      " 161  0.278 -0.831 -1.682  1.172 -0.595  0.211   0.4308126240\n",
      " 163  0.278 -0.831 -1.682  1.172 -0.595  0.179   0.4307246889\n",
      " 165  0.278 -0.831 -1.682  1.172 -0.595  0.167   0.4307008851\n",
      " 166  0.278 -0.831 -1.682  1.172 -0.595  0.164   0.4306967806\n",
      " 167  0.278 -0.831 -1.682  1.172 -0.595  0.157   0.4306795882\n",
      " 168  0.278 -0.831 -1.682  1.172 -0.595  0.153   0.4306670011\n",
      " 171  0.278 -0.831 -1.682  1.172 -0.595  0.152   0.4306639691\n",
      "  powell nthiter 2: fret = 0.430664\n",
      " 179  0.020 -0.831 -1.682  1.172 -0.595  0.152   0.4258094636\n",
      " 180  0.026 -0.831 -1.682  1.172 -0.595  0.152   0.4257497866\n",
      " 181  0.066 -0.831 -1.682  1.172 -0.595  0.152   0.4253962352\n",
      " 183  0.093 -0.831 -1.682  1.172 -0.595  0.152   0.4253189893\n",
      " 190  0.093 -1.449 -1.682  1.172 -0.595  0.152   0.4019162006\n",
      " 194  0.093 -1.435 -1.682  1.172 -0.595  0.152   0.4018596128\n",
      " 205  0.093 -1.435 -1.300  1.172 -0.595  0.152   0.4014473121\n",
      " 206  0.093 -1.435 -1.476  1.172 -0.595  0.152   0.3996133908\n",
      " 207  0.093 -1.435 -1.481  1.172 -0.595  0.152   0.3995479050\n",
      " 208  0.093 -1.435 -1.558  1.172 -0.595  0.152   0.3990759779\n",
      " 210  0.093 -1.435 -1.556  1.172 -0.595  0.152   0.3990750340\n",
      " 211  0.093 -1.435 -1.554  1.172 -0.595  0.152   0.3990737958\n",
      " 223  0.093 -1.435 -1.554  1.339 -0.595  0.152   0.3956702942\n",
      " 224  0.093 -1.435 -1.554  1.342 -0.595  0.152   0.3956612377\n",
      " 225  0.093 -1.435 -1.554  1.353 -0.595  0.152   0.3956384165\n",
      " 228  0.093 -1.435 -1.554  1.354 -0.595  0.152   0.3956375087\n",
      " 229  0.093 -1.435 -1.554  1.358 -0.595  0.152   0.3956366906\n",
      " 231  0.093 -1.435 -1.554  1.357 -0.595  0.152   0.3956365324\n",
      " 239  0.093 -1.435 -1.554  1.357 -0.656  0.152   0.3929882233\n",
      " 241  0.093 -1.435 -1.554  1.357 -0.694  0.152   0.3922126645\n",
      " 243  0.093 -1.435 -1.554  1.357 -0.690  0.152   0.3921999242\n",
      " 244  0.093 -1.435 -1.554  1.357 -0.691  0.152   0.3921975511\n",
      " 252  0.093 -1.435 -1.554  1.357 -0.691 -0.079   0.3877731294\n",
      "  powell nthiter 3: fret = 0.387773\n",
      " 265 -0.011 -1.435 -1.554  1.357 -0.691 -0.079   0.3844648717\n",
      " 267 -0.004 -1.435 -1.554  1.357 -0.691 -0.079   0.3844462885\n",
      " 268 -0.003 -1.435 -1.554  1.357 -0.691 -0.079   0.3844440295\n",
      " 269  0.000 -1.435 -1.554  1.357 -0.691 -0.079   0.3844439799\n",
      " 272 -0.001 -1.435 -1.554  1.357 -0.691 -0.079   0.3844431152\n",
      " 279 -0.001 -1.414 -1.554  1.357 -0.691 -0.079   0.3841491837\n",
      " 280 -0.001 -1.381 -1.554  1.357 -0.691 -0.079   0.3838816667\n",
      " 283 -0.001 -1.382 -1.554  1.357 -0.691 -0.079   0.3838801552\n",
      " 284 -0.001 -1.384 -1.554  1.357 -0.691 -0.079   0.3838801069\n",
      " 294 -0.001 -1.384 -1.594  1.357 -0.691 -0.079   0.3832797641\n",
      " 296 -0.001 -1.384 -1.596  1.357 -0.691 -0.079   0.3832785166\n",
      " 308 -0.001 -1.384 -1.596  1.358 -0.691 -0.079   0.3832778113\n",
      " 316 -0.001 -1.384 -1.596  1.358 -0.719 -0.079   0.3826361548\n",
      " 328 -0.001 -1.384 -1.596  1.358 -0.719 -0.124   0.3822837046\n",
      " 329 -0.001 -1.384 -1.596  1.358 -0.719 -0.125   0.3822818190\n",
      " 331 -0.001 -1.384 -1.596  1.358 -0.719 -0.128   0.3822790938\n",
      " 332 -0.001 -1.384 -1.596  1.358 -0.719 -0.129   0.3822783936\n",
      " 333 -0.001 -1.384 -1.596  1.358 -0.719 -0.130   0.3822778697\n",
      " 340 -0.037 -1.365 -1.613  1.358 -0.730 -0.149   0.3815185274\n",
      " 342 -0.039 -1.364 -1.614  1.358 -0.730 -0.150   0.3815149976\n",
      " 343 -0.039 -1.363 -1.614  1.358 -0.730 -0.151   0.3815147584\n",
      " 344 -0.039 -1.363 -1.614  1.358 -0.730 -0.151   0.3815147209\n",
      " 345 -0.039 -1.363 -1.614  1.358 -0.730 -0.151   0.3815143416\n",
      "  powell nthiter 4: fret = 0.381514\n",
      " 363 -0.039 -1.367 -1.614  1.358 -0.730 -0.151   0.3814838418\n",
      " 366 -0.039 -1.373 -1.614  1.358 -0.730 -0.151   0.3814614805\n",
      " 377 -0.039 -1.373 -1.595  1.358 -0.730 -0.151   0.3813433824\n",
      " 378 -0.039 -1.373 -1.594  1.358 -0.730 -0.151   0.3813430900\n",
      " 388 -0.039 -1.373 -1.594  1.357 -0.730 -0.151   0.3813390882\n",
      " 389 -0.039 -1.373 -1.594  1.351 -0.730 -0.151   0.3813317279\n",
      " 391 -0.039 -1.373 -1.594  1.353 -0.730 -0.151   0.3813309805\n",
      " 401 -0.039 -1.373 -1.594  1.353 -0.726 -0.151   0.3813137393\n",
      " 402 -0.039 -1.373 -1.594  1.353 -0.725 -0.151   0.3813129821\n",
      " 410 -0.049 -1.368 -1.599  1.353 -0.728 -0.156   0.3812740218\n",
      " 411 -0.049 -1.368 -1.598  1.353 -0.728 -0.156   0.3812726540\n",
      " 413 -0.048 -1.369 -1.598  1.353 -0.728 -0.156   0.3812719773\n",
      " 415 -0.048 -1.369 -1.598  1.353 -0.728 -0.156   0.3812715917\n",
      "  powell nthiter 5: fret = 0.381272\n",
      " 438 -0.048 -1.377 -1.598  1.353 -0.728 -0.156   0.3812483580\n",
      " 439 -0.048 -1.374 -1.598  1.353 -0.728 -0.156   0.3812478468\n",
      " 441 -0.048 -1.375 -1.598  1.353 -0.728 -0.156   0.3812470975\n",
      " 450 -0.048 -1.375 -1.593  1.353 -0.728 -0.156   0.3812325771\n",
      " 451 -0.048 -1.375 -1.591  1.353 -0.728 -0.156   0.3812323246\n",
      " 462 -0.048 -1.375 -1.591  1.347 -0.728 -0.156   0.3812252894\n",
      " 482 -0.056 -1.371 -1.594  1.347 -0.730 -0.160   0.3812218208\n",
      " 483 -0.052 -1.373 -1.593  1.347 -0.729 -0.158   0.3812169961\n",
      " 484 -0.052 -1.373 -1.593  1.347 -0.729 -0.158   0.3812169933\n",
      " 485 -0.052 -1.373 -1.593  1.347 -0.729 -0.158   0.3812169474\n",
      " 487 -0.052 -1.373 -1.593  1.347 -0.729 -0.158   0.3812169043\n",
      " 491 -0.055 -1.378 -1.587  1.342 -0.730 -0.159   0.3811904082\n",
      " 496 -0.057 -1.381 -1.583  1.339 -0.731 -0.161   0.3811864488\n",
      " 499 -0.057 -1.381 -1.583  1.339 -0.731 -0.161   0.3811862098\n",
      "  powell nthiter 6: fret = 0.381186\n",
      " 512 -0.057 -1.381 -1.583  1.339 -0.731 -0.190   0.3811165310\n",
      " 514 -0.057 -1.381 -1.583  1.339 -0.731 -0.184   0.3811114935\n",
      " 518 -0.057 -1.381 -1.583  1.339 -0.731 -0.183   0.3811113979\n",
      " 526 -0.070 -1.374 -1.589  1.339 -0.735 -0.190   0.3810498957\n",
      " 527 -0.070 -1.375 -1.589  1.339 -0.734 -0.190   0.3810491550\n",
      " 528 -0.069 -1.375 -1.589  1.339 -0.734 -0.189   0.3810473060\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " 530 -0.067 -1.376 -1.588  1.339 -0.733 -0.189   0.3810470752\n",
      " 534 -0.067 -1.376 -1.588  1.339 -0.734 -0.189   0.3810470458\n",
      " 545 -0.067 -1.376 -1.582  1.339 -0.734 -0.189   0.3810382313\n",
      " 547 -0.067 -1.376 -1.583  1.339 -0.734 -0.189   0.3810381493\n",
      " 557 -0.067 -1.376 -1.583  1.340 -0.734 -0.189   0.3810348829\n",
      " 558 -0.067 -1.376 -1.583  1.342 -0.734 -0.189   0.3810319964\n",
      " 560 -0.067 -1.376 -1.583  1.341 -0.734 -0.189   0.3810302859\n",
      " 571 -0.067 -1.376 -1.583  1.341 -0.733 -0.189   0.3810287062\n",
      " 572 -0.067 -1.376 -1.583  1.341 -0.732 -0.189   0.3810284937\n",
      " 574 -0.071 -1.381 -1.578  1.336 -0.733 -0.191   0.3809685954\n",
      " 575 -0.077 -1.389 -1.568  1.327 -0.734 -0.194   0.3809204837\n",
      " 576 -0.078 -1.391 -1.566  1.325 -0.735 -0.195   0.3809124335\n",
      " 579 -0.080 -1.393 -1.563  1.322 -0.735 -0.195   0.3809101681\n",
      " 584 -0.080 -1.393 -1.563  1.322 -0.735 -0.195   0.3809100355\n",
      " 591 -0.108 -1.413 -1.534  1.297 -0.742 -0.233   0.3806339879\n",
      " 599 -0.108 -1.413 -1.534  1.297 -0.742 -0.233   0.3806339325\n",
      " 600 -0.108 -1.413 -1.534  1.297 -0.742 -0.233   0.3806335654\n",
      " 601 -0.107 -1.413 -1.534  1.297 -0.742 -0.233   0.3806334613\n",
      "  powell nthiter 7: fret = 0.380633\n",
      " 613 -0.107 -1.413 -1.534  1.297 -0.742 -0.304   0.3804533369\n",
      " 614 -0.107 -1.413 -1.534  1.297 -0.742 -0.286   0.3802951247\n",
      " 615 -0.107 -1.413 -1.534  1.297 -0.742 -0.274   0.3802606069\n",
      " 617 -0.107 -1.413 -1.534  1.297 -0.742 -0.276   0.3802601422\n",
      " 625 -0.124 -1.404 -1.542  1.297 -0.747 -0.284   0.3800437585\n",
      " 626 -0.124 -1.404 -1.542  1.297 -0.747 -0.285   0.3800414876\n",
      " 627 -0.128 -1.402 -1.544  1.297 -0.748 -0.287   0.3800275096\n",
      " 629 -0.130 -1.401 -1.545  1.297 -0.749 -0.288   0.3800260314\n",
      " 630 -0.130 -1.401 -1.545  1.297 -0.749 -0.288   0.3800260219\n",
      " 631 -0.130 -1.401 -1.545  1.297 -0.748 -0.288   0.3800259208\n",
      " 645 -0.130 -1.401 -1.543  1.297 -0.748 -0.288   0.3800253238\n",
      " 655 -0.130 -1.401 -1.543  1.319 -0.748 -0.288   0.3799944937\n",
      " 656 -0.130 -1.401 -1.543  1.310 -0.748 -0.288   0.3799498499\n",
      " 657 -0.130 -1.401 -1.543  1.309 -0.748 -0.288   0.3799486184\n",
      " 658 -0.130 -1.401 -1.543  1.308 -0.748 -0.288   0.3799476008\n",
      " 677 -0.125 -1.397 -1.548  1.312 -0.747 -0.281   0.3799279449\n",
      " 681 -0.125 -1.397 -1.549  1.312 -0.747 -0.281   0.3799277605\n",
      "  powell nthiter 8: fret = 0.379928\n",
      " 695 -0.125 -1.397 -1.549  1.312 -0.747 -0.288   0.3799011116\n",
      " 696 -0.125 -1.397 -1.549  1.312 -0.747 -0.295   0.3798909753\n",
      " 705 -0.126 -1.396 -1.549  1.312 -0.748 -0.296   0.3798831413\n",
      " 706 -0.129 -1.395 -1.551  1.312 -0.749 -0.298   0.3798729153\n",
      " 708 -0.132 -1.393 -1.552  1.312 -0.749 -0.299   0.3798700693\n",
      " 709 -0.132 -1.393 -1.552  1.312 -0.750 -0.299   0.3798698573\n",
      " 723 -0.132 -1.393 -1.551  1.312 -0.750 -0.299   0.3798676623\n",
      " 724 -0.132 -1.393 -1.548  1.312 -0.750 -0.299   0.3798649372\n",
      " 757 -0.131 -1.392 -1.550  1.314 -0.749 -0.297   0.3798629370\n",
      "  powell nthiter 9: fret = 0.379863\n",
      " 776 -0.131 -1.392 -1.550  1.314 -0.749 -0.298   0.3798610937\n",
      " 785 -0.131 -1.392 -1.550  1.314 -0.749 -0.298   0.3798608691\n",
      " 798 -0.131 -1.392 -1.549  1.314 -0.749 -0.298   0.3798603948\n",
      " 828 -0.130 -1.392 -1.549  1.314 -0.749 -0.298   0.3798602833\n",
      " 830 -0.130 -1.392 -1.549  1.314 -0.749 -0.298   0.3798601430\n",
      "Powell done niters = 9\n",
      "Computing relative cost\n",
      " 0  -25.0 -25.0 -25.0   1.020693\n",
      " 1  -25.0 -25.0  25.0   1.005424\n",
      " 2  -25.0  25.0 -25.0   0.999220\n",
      " 3  -25.0  25.0  25.0   0.988467\n",
      " 4   25.0 -25.0 -25.0   1.035120\n",
      " 5   25.0 -25.0  25.0   1.053021\n",
      " 6   25.0  25.0 -25.0   1.094575\n",
      " 7   25.0  25.0  25.0   1.035329\n",
      "REL:  8  0.379860    8.231848  1.028981 rel = 0.369161 \n",
      "Number of iterations     9\n",
      "Min cost was 0.379860\n",
      "Number of FunctionCalls   836\n",
      "TolPowell 0.000100\n",
      "nMaxItersPowell 36\n",
      "OptimizationTime 0.753000 sec\n",
      "Parameters at optimum (transmm) -0.13017 -1.39207 -1.54905\n",
      "Parameters at optimum (rotdeg)  1.31398 -0.74902 -0.29772 \n",
      "Final costs ----------------\n",
      "Number of surface hits 1644\n",
      "WM  Intensity   740.3647 +/- 115.7223\n",
      "Ctx Intensity   817.0991 +/- 165.3876\n",
      "Pct Contrast      8.3284 +/-  21.9894\n",
      "Cost   0.3799\n",
      "RelCost   0.5807\n",
      "Reg at min cost was \n",
      " 0.99937   0.03558  -0.00153   1.29329;\n",
      " 0.01094  -0.26581   0.96396  -20.79675;\n",
      "-0.03389   0.96337   0.26603   5.50538;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Writing optimal reg to bold/tmp.bbregister.27486/bbr.pass1.dat, type = 14 \n",
      "Original Reg \n",
      " 0.99877   0.04955  -0.00306   1.61636;\n",
      " 0.01505  -0.24347   0.96979  -19.23062;\n",
      "-0.04731   0.96864   0.24392   7.47685;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Original Reg - Optimal Reg\n",
      "-0.00060   0.01397  -0.00153   0.32307;\n",
      " 0.00411   0.02234   0.00583   1.56613;\n",
      "-0.01342   0.00527  -0.02211   1.97147;\n",
      " 0.00000   0.00000   0.00000   0.00000;\n",
      "\n",
      "Computing change in lh position\n",
      "LH rmsDiffMean 2.000440\n",
      "Computing change in rh position\n",
      "Surface-RMS-Diff-mm 1.890073 0.638778 3.564877\n",
      "mri_segreg done\n",
      "mri_segreg --mov bold/tmp.bbregister.27486/template.nii --init-reg bold/tmp.bbregister.27486/bbr.pass1.dat --out-reg bold/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/tmp.bbregister.27486/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5\n",
      "$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/hands/Sess01\n",
      "mri_segreg --mov bold/tmp.bbregister.27486/template.nii --init-reg bold/tmp.bbregister.27486/bbr.pass1.dat --out-reg bold/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/tmp.bbregister.27486/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "movvol bold/tmp.bbregister.27486/template.nii\n",
      "regfile bold/tmp.bbregister.27486/bbr.pass1.dat\n",
      "subject pBrain\n",
      "dof 6\n",
      "outregfile bold/register.dof6.dat\n",
      "UseMask 0\n",
      "UseLH 1\n",
      "UseRH 1\n",
      "nsubsamp 1\n",
      "PenaltySign  -1\n",
      "PenaltySlope 0.500000\n",
      "PenaltyCenter 0.000000\n",
      "surfname white\n",
      "GMProjFrac 0.500000\n",
      "WMProjAbs 2.000000\n",
      "lhcostfile (null)\n",
      "rhcostfile (null)\n",
      "interp  trilinear (1)\n",
      "frame  0\n",
      "TolPowell 0.000000\n",
      "nMaxItersPowell 36\n",
      "n1dmin  3\n",
      "Profile   0\n",
      "Gdiag_no  -1\n",
      "AddNoise  0 (0)\n",
      "SynthSeed 1511884478\n",
      "TransRandMax 0.000000\n",
      "RotRandMax 0.000000\n",
      "Translations 0.000000 0.000000 0.000000\n",
      "Rotations   0.000000 0.000000 0.000000\n",
      "Input reg\n",
      " 0.99937   0.03558  -0.00153   1.29329;\n",
      " 0.01094  -0.26581   0.96396  -20.79675;\n",
      "-0.03389   0.96337   0.26603   5.50538;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Loading mov\n",
      "Projecting LH Surfs\n",
      "Loading lh.white surf\n",
      "Loading lh.thickness for GM\n",
      "GM Proj: 1 0.500000 2.000000\n",
      "WM Proj: 0 0.500000 2.000000\n",
      "Projecting RH Surfs\n",
      "Loading rh.white surf\n",
      "Loading rh.thickness for GM\n",
      "Projecting RH Surfs\n",
      "Using lh.cortex.label\n",
      "Using rh.cortex.label\n",
      "Computing relative cost\n",
      " 0  -25.0 -25.0 -25.0   1.025577\n",
      " 1  -25.0 -25.0  25.0   1.006807\n",
      " 2  -25.0  25.0 -25.0   1.038062\n",
      " 3  -25.0  25.0  25.0   1.020296\n",
      " 4   25.0 -25.0 -25.0   1.017456\n",
      " 5   25.0 -25.0  25.0   1.037416\n",
      " 6   25.0  25.0 -25.0   1.032043\n",
      " 7   25.0  25.0  25.0   1.026820\n",
      "REL:  8  0.379854    8.204476  1.025560 rel = 0.370387 \n",
      "Initial costs ----------------\n",
      "Number of surface hits 164022\n",
      "WM  Intensity   740.6241 +/- 117.0804\n",
      "Ctx Intensity   819.6752 +/- 165.8489\n",
      "Pct Contrast      8.5521 +/-  21.9173\n",
      "Cost   0.3799\n",
      "RelCost   0.3704\n",
      "\n",
      "------------------------------------\n",
      "Brute force preopt -0.1 0.1 0.1, n = 729\n",
      "     0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.3905   0.3905  0.0\n",
      "     1  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000   0.0000      0.3903   0.3903  0.0\n",
      "     3  -0.1000  -0.1000  -0.1000  -0.1000   0.0000  -0.1000      0.3898   0.3898  0.0\n",
      "     9  -0.1000  -0.1000  -0.1000   0.0000  -0.1000  -0.1000      0.3882   0.3882  0.0\n",
      "    10  -0.1000  -0.1000  -0.1000   0.0000  -0.1000   0.0000      0.3872   0.3872  0.0\n",
      "    19  -0.1000  -0.1000  -0.1000   0.1000  -0.1000   0.0000      0.3871   0.3871  0.0\n",
      "    30  -0.1000  -0.1000   0.0000  -0.1000   0.0000  -0.1000      0.3862   0.3862  0.0\n",
      "    57  -0.1000  -0.1000   0.1000  -0.1000   0.0000  -0.1000      0.3857   0.3857  0.0\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "    90  -0.1000   0.0000  -0.1000   0.0000  -0.1000  -0.1000      0.3840   0.3840  0.0\n",
      "    91  -0.1000   0.0000  -0.1000   0.0000  -0.1000   0.0000      0.3829   0.3829  0.0\n",
      "   118  -0.1000   0.0000   0.0000   0.0000  -0.1000   0.0000      0.3826   0.3826  0.0\n",
      "   337   0.0000   0.0000  -0.1000   0.0000   0.0000   0.0000      0.3820   0.3820  0.0\n",
      "   363   0.0000   0.0000   0.0000   0.0000   0.0000  -0.1000      0.3819   0.3819  0.0\n",
      "   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.3799   0.3799  0.0\n",
      "Brute Force --------------------------\n",
      "Min cost was 0.379860\n",
      "Number of iterations   729\n",
      "Search time 0.601000 sec\n",
      "Parameters at best (transmm, rotdeg)\n",
      "  0.000   0.000   0.000  0.000  0.000  0.000 \n",
      "--------------------------------------------\n",
      "\n",
      "Starting Powell Minimization\n",
      "Init Powel Params dof = 6\n",
      "0 0\n",
      "1 0\n",
      "2 0\n",
      "3 0\n",
      "4 0\n",
      "5 0\n",
      "fs_powell::minimize\n",
      "  nparams 6\n",
      "  maxfev 36\n",
      "  ftol   0.000000\n",
      "  linmin_xtol_   0.001000\n",
      "  powell nthiter 0: fret = 0.379854\n",
      "   7 -0.040  0.000  0.000  0.000  0.000  0.000   0.3796710455\n",
      "   8 -0.053  0.000  0.000  0.000  0.000  0.000   0.3796628809\n",
      "   9 -0.051  0.000  0.000  0.000  0.000  0.000   0.3796622473\n",
      "  10 -0.050  0.000  0.000  0.000  0.000  0.000   0.3796622314\n",
      "  18 -0.050  0.134  0.000  0.000  0.000  0.000   0.3783300856\n",
      "  30 -0.050  0.134 -0.208  0.000  0.000  0.000   0.3762035186\n",
      "  31 -0.050  0.134 -0.191  0.000  0.000  0.000   0.3762018509\n",
      "  32 -0.050  0.134 -0.199  0.000  0.000  0.000   0.3762005306\n",
      "  33 -0.050  0.134 -0.198  0.000  0.000  0.000   0.3762004026\n",
      "  41 -0.050  0.134 -0.198 -0.100  0.000  0.000   0.3752732332\n",
      "  42 -0.050  0.134 -0.198 -0.122  0.000  0.000   0.3752563779\n",
      "  45 -0.050  0.134 -0.198 -0.120  0.000  0.000   0.3752541845\n",
      "  54 -0.050  0.134 -0.198 -0.120  0.107  0.000   0.3741780839\n",
      "  55 -0.050  0.134 -0.198 -0.120  0.117  0.000   0.3741357161\n",
      "  56 -0.050  0.134 -0.198 -0.120  0.151  0.000   0.3741029285\n",
      "  58 -0.050  0.134 -0.198 -0.120  0.141  0.000   0.3740944901\n",
      "  67 -0.050  0.134 -0.198 -0.120  0.141  0.082   0.3736612965\n",
      "  68 -0.050  0.134 -0.198 -0.120  0.141  0.098   0.3736464060\n",
      "  71 -0.050  0.134 -0.198 -0.120  0.141  0.097   0.3736444231\n",
      "  powell nthiter 1: fret = 0.373644\n",
      "  80  0.039  0.134 -0.198 -0.120  0.141  0.097   0.3732325860\n",
      "  81  0.029  0.134 -0.198 -0.120  0.141  0.097   0.3732098209\n",
      "  82  0.021  0.134 -0.198 -0.120  0.141  0.097   0.3732000397\n",
      "  83  0.016  0.134 -0.198 -0.120  0.141  0.097   0.3731991405\n",
      "  84  0.017  0.134 -0.198 -0.120  0.141  0.097   0.3731990447\n",
      "  92  0.017  0.177 -0.198 -0.120  0.141  0.097   0.3730250917\n",
      " 103  0.017  0.177 -0.170 -0.120  0.141  0.097   0.3728847059\n",
      " 104  0.017  0.177 -0.149 -0.120  0.141  0.097   0.3728302611\n",
      " 107  0.017  0.177 -0.145 -0.120  0.141  0.097   0.3728277594\n",
      " 116  0.017  0.177 -0.145 -0.134  0.141  0.097   0.3728083643\n",
      " 118  0.017  0.177 -0.145 -0.132  0.141  0.097   0.3728060361\n",
      " 128  0.017  0.177 -0.145 -0.132  0.149  0.097   0.3727982947\n",
      " 137  0.017  0.177 -0.145 -0.132  0.149  0.108   0.3727716673\n",
      " 138  0.017  0.177 -0.145 -0.132  0.149  0.128   0.3727449516\n",
      " 140  0.017  0.177 -0.145 -0.132  0.149  0.138   0.3727257377\n",
      " 144  0.017  0.177 -0.145 -0.132  0.149  0.135   0.3727240961\n",
      "  powell nthiter 2: fret = 0.372724\n",
      " 155  0.019  0.177 -0.145 -0.132  0.149  0.135   0.3727235600\n",
      " 156  0.021  0.177 -0.145 -0.132  0.149  0.135   0.3727233664\n",
      " 159  0.020  0.177 -0.145 -0.132  0.149  0.135   0.3727233288\n",
      " 178  0.020  0.177 -0.137 -0.132  0.149  0.135   0.3727219425\n",
      " 179  0.020  0.177 -0.140 -0.132  0.149  0.135   0.3727214744\n",
      " 192  0.020  0.177 -0.140 -0.130  0.149  0.135   0.3727206493\n",
      " 193  0.020  0.177 -0.140 -0.129  0.149  0.135   0.3727205260\n",
      " 201  0.020  0.177 -0.140 -0.129  0.151  0.135   0.3727199415\n",
      " 202  0.020  0.177 -0.140 -0.129  0.153  0.135   0.3727199324\n",
      "  powell nthiter 3: fret = 0.372720\n",
      " 247  0.020  0.177 -0.141 -0.129  0.153  0.135   0.3727198631\n",
      "  powell nthiter 4: fret = 0.372720\n",
      "Powell done niters = 4\n",
      "Computing relative cost\n",
      " 0  -25.0 -25.0 -25.0   1.022787\n",
      " 1  -25.0 -25.0  25.0   1.007841\n",
      " 2  -25.0  25.0 -25.0   1.037818\n",
      " 3  -25.0  25.0  25.0   1.021453\n",
      " 4   25.0 -25.0 -25.0   1.016968\n",
      " 5   25.0 -25.0  25.0   1.038979\n",
      " 6   25.0  25.0 -25.0   1.033540\n",
      " 7   25.0  25.0  25.0   1.027230\n",
      "REL:  8  0.372720    8.206616  1.025827 rel = 0.363336 \n",
      "Number of iterations     4\n",
      "Min cost was 0.372720\n",
      "Number of FunctionCalls   343\n",
      "TolPowell 0.000000\n",
      "nMaxItersPowell 36\n",
      "OptimizationTime 13.681000 sec\n",
      "Parameters at optimum (transmm)  0.02003  0.17660 -0.14100\n",
      "Parameters at optimum (rotdeg) -0.12949  0.15257  0.13483 \n",
      "Final costs ----------------\n",
      "Number of surface hits 163573\n",
      "WM  Intensity   741.0763 +/- 114.8013\n",
      "Ctx Intensity   821.7606 +/- 163.8580\n",
      "Pct Contrast      8.7803 +/-  21.7189\n",
      "Cost   0.3727\n",
      "RelCost   0.3704\n",
      "Reg at min cost was \n",
      " 0.99924   0.03876  -0.00310   1.37700;\n",
      " 0.01321  -0.26354   0.96456  -20.60452;\n",
      "-0.03657   0.96387   0.26385   5.40790;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Writing optimal reg to bold/register.dof6.dat, type = 14 \n",
      "Original Reg \n",
      " 0.99937   0.03558  -0.00153   1.29329;\n",
      " 0.01094  -0.26581   0.96396  -20.79675;\n",
      "-0.03389   0.96337   0.26603   5.50538;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Original Reg - Optimal Reg\n",
      " 0.00012  -0.00319   0.00157  -0.08371;\n",
      "-0.00227  -0.00227  -0.00059  -0.19223;\n",
      " 0.00269  -0.00050   0.00218   0.09748;\n",
      " 0.00000   0.00000   0.00000   0.00000;\n",
      "\n",
      "Computing change in lh position\n",
      "LH rmsDiffMean 0.212280\n",
      "Computing change in rh position\n",
      "Surface-RMS-Diff-mm 0.287842 0.106568 0.501698\n",
      "mri_segreg done\n",
      "MinCost: 0.372720 741.076271 821.760642 8.780308 \n",
      "tkregister2_cmdl --mov bold/template.nii.gz --reg bold/register.dof6.dat --noedit --ltaout bold/register.dof6.lta\n",
      "tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl\n",
      "INFO: no target volume specified, assuming FreeSurfer orig volume.\n",
      "target  volume orig\n",
      "movable volume bold/template.nii.gz\n",
      "reg file       bold/register.dof6.dat\n",
      "LoadVol        0\n",
      "ZeroCRAS       0\n",
      "$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $\n",
      "Diagnostic Level -1\n",
      "---- Input registration matrix --------\n",
      " 0.99924   0.03876  -0.00310   1.37700;\n",
      " 0.01321  -0.26354   0.96456  -20.60452;\n",
      "-0.03657   0.96387   0.26385   5.40790;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "float2int = 0\n",
      "---------------------------------------\n",
      "INFO: loading target /usr/local/freesurfer/subjects/pBrain/mri/orig.mgz\n",
      "Ttarg: --------------------\n",
      "-1.00000   0.00000   0.00000   128.00000;\n",
      " 0.00000   0.00000   1.00000  -128.00000;\n",
      " 0.00000  -1.00000   0.00000   128.00000;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "INFO: loading movable bold/template.nii.gz\n",
      "Tmov: --------------------\n",
      "-2.00000   0.00000   0.00000   128.00000;\n",
      " 0.00000   0.00000   2.00000  -40.00000;\n",
      " 0.00000  -2.00000   0.00000   128.00000;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "mkheaderreg = 0, float2int = 0\n",
      "---- Input registration matrix --------\n",
      " 0.99924   0.03876  -0.00310   1.37700;\n",
      " 0.01321  -0.26354   0.96456  -20.60452;\n",
      "-0.03657   0.96387   0.26385   5.40790;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Determinant -1\n",
      "subject = pBrain\n",
      "RegMat ---------------------------\n",
      " 0.99924   0.03876  -0.00310   1.37700;\n",
      " 0.01321  -0.26354   0.96456  -20.60452;\n",
      "-0.03657   0.96387   0.26385   5.40790;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Cleaning up\n",
      " \n",
      "Started at Fri Nov 24 13:05:54 CET 2017 \n",
      "Ended   at Fri Nov 24 13:07:03 CET 2017\n",
      "BBR-Run-Time-Sec 69\n",
      " \n",
      "bbregister Done\n",
      "To check results, run:\n",
      "tkregisterfv --mov bold/template.nii.gz --reg bold/register.dof6.lta --surfs \n",
      " \n",
      "  Run: 005 ----------------\n",
      "Fri Nov 24 13:07:03 CET 2017\n",
      "--------------------------------------\n",
      "/data/martin/prosopagnosia/hands/Sess01\n",
      "bbregister --s pBrain --init-coreg --6 --bold --mov bold/005/template.nii.gz --reg bold/005/register.dof6.dat --lta bold/005/register.dof6.lta --init-reg-out bold/005/init.register.dof6.dat\n",
      "tmp bold/005/tmp.bbregister.27643\n",
      "Log file is bold/005/register.dof6.dat.log\n",
      "Fri Nov 24 13:07:04 CET 2017\n",
      "\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/hands/Sess01\n",
      "/usr/local/freesurfer/bin/bbregister --s pBrain --init-coreg --6 --bold --mov bold/005/template.nii.gz --reg bold/005/register.dof6.dat --lta bold/005/register.dof6.lta --init-reg-out bold/005/init.register.dof6.dat\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "FREESURFER_HOME /usr/local/freesurfer\n",
      "mri_convert bold/005/template.nii.gz bold/005/tmp.bbregister.27643/template.nii\n",
      "mri_convert.bin bold/005/template.nii.gz bold/005/tmp.bbregister.27643/template.nii \n",
      "$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $\n",
      "reading from bold/005/template.nii.gz...\n",
      "TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00\n",
      "i_ras = (-0.999463, -0.0273032, 0.0181267)\n",
      "j_ras = (0.022681, -0.975511, -0.21878)\n",
      "k_ras = (0.0236561, -0.218251, 0.975606)\n",
      "writing to bold/005/tmp.bbregister.27643/template.nii...\n",
      "mri_coreg --s pBrain --mov bold/005/tmp.bbregister.27643/template.nii --regdat bold/005/tmp.bbregister.27643/reg.init.dat --reg bold/005/tmp.bbregister.27643/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01\n",
      "\n",
      "$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/hands/Sess01\n",
      "cmdline mri_coreg --s pBrain --mov bold/005/tmp.bbregister.27643/template.nii --regdat bold/005/tmp.bbregister.27643/reg.init.dat --reg bold/005/tmp.bbregister.27643/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "dof    6\n",
      "nsep    1\n",
      "cras0    1\n",
      "ftol    0.000100\n",
      "linmintol    0.010000\n",
      "bf       1\n",
      "bflim    30.000000\n",
      "bfnsamp    30\n",
      "SmoothRef 0\n",
      "SatPct    99.990000\n",
      "MovOOB 0\n",
      "optschema 1\n",
      "Reading in mov bold/005/tmp.bbregister.27643/template.nii\n",
      "Reading in ref /usr/local/freesurfer/subjects/pBrain/mri/brainmask.mgz\n",
      "Reading in and applying refmask /usr/local/freesurfer/subjects/pBrain/mri/aparc+aseg.mgz\n",
      "Setting cras translation parameters to align centers\n",
      "Creating random numbers for coordinate dithering\n",
      "Performing intensity dithering\n",
      "Initial parameters  4.8266 -14.2690  7.8386  0.0000  0.0000  0.0000  1.0000  1.0000  1.0000  0.0000  0.0000  0.0000 \n",
      "Separation list (1):  4   min = 4\n",
      "DoSmoothing 1\n",
      "DoCoordDither 1\n",
      "DoIntensityDither 1\n",
      "nitersmax 4\n",
      "ftol 1.000e-04\n",
      "linmintol 1.000e-02\n",
      "SatPct 99.990000\n",
      "Hist FWHM 7.000000 7.000000\n",
      "nthreads 1\n",
      "movsat = 1710.6666\n",
      "mov gstd 1.6917 1.6917 1.6917\n",
      "Smoothing mov\n",
      "refsat = 115.0000\n",
      "ref gstd 1.8914 1.8914 1.8914\n",
      "Smoothing ref\n",
      "COREGpreproc() done\n",
      "Testing if mov and target overlap\n",
      "Init cost   -1.0426049272\n",
      "nhits = 78038 out of 16777216, Percent Overlap:  29.8\n",
      "Initial  RefRAS-to-MovRAS\n",
      " 1.00000   0.00000   0.00000   4.82664;\n",
      " 0.00000   1.00000   0.00000  -14.26899;\n",
      " 0.00000   0.00000   1.00000   7.83862;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Initial  RefVox-to-MovVox\n",
      " 0.49973  -0.00906  -0.01365   2.68039;\n",
      "-0.01134   0.10939  -0.48776   113.18749;\n",
      "-0.01183  -0.48780  -0.10913   97.11647;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "sep = 4 -----------------------------------\n",
      "COREGoptBruteForce() 30 1 30\n",
      "Turning on MovOOB for BruteForce Search\n",
      "#BF# sep= 4 iter=0 lim=30.0 delta=2.00   4.82664  -0.26899 -10.16138   2.00000   2.00000   0.00000   -1.0313576\n",
      "Turning  MovOOB back off after brute force search\n",
      "\n",
      "\n",
      "---------------------------------\n",
      "Init Powel Params dof = 6\n",
      "Starting OpenPowel2(), sep = 4\n",
      "InitialCost        -1.0694402456 \n",
      "#@#  4  188  4.82664 -0.26899 -10.16138 2.00000 2.00000 0.00000   -1.0694402\n",
      "fs_powell::minimize\n",
      "  nparams 6\n",
      "  maxfev 4\n",
      "  ftol   0.000100\n",
      "  linmin_xtol_   0.010000\n",
      "  powell nthiter 0: fret = -1.069440\n",
      "#@#  4  195  4.81472 -0.26899 -10.16138 2.00000 2.00000 0.00000   -1.0694406\n",
      "#@#  4  200  4.81472 -1.88702 -10.16138 2.00000 2.00000 0.00000   -1.0716926\n",
      "#@#  4  203  4.81472 -6.11132 -10.16138 2.00000 2.00000 0.00000   -1.0718940\n",
      "#@#  4  205  4.81472 -4.08611 -10.16138 2.00000 2.00000 0.00000   -1.0732653\n",
      "#@#  4  212  4.81472 -4.08611 -9.16138 2.00000 2.00000 0.00000   -1.0742503\n",
      "#@#  4  213  4.81472 -4.08611 -7.54335 2.00000 2.00000 0.00000   -1.0743387\n",
      "#@#  4  214  4.81472 -4.08611 -8.27556 2.00000 2.00000 0.00000   -1.0745175\n",
      "#@#  4  219  4.81472 -4.08611 -8.40480 2.00000 2.00000 0.00000   -1.0745330\n",
      "#@#  4  221  4.81472 -4.08611 -8.38892 2.00000 2.00000 0.00000   -1.0745381\n",
      "#@#  4  228  4.81472 -4.08611 -8.38892 1.38197 2.00000 0.00000   -1.0745711\n",
      "#@#  4  230  4.81472 -4.08611 -8.38892 1.60109 2.00000 0.00000   -1.0745838\n",
      "#@#  4  231  4.81472 -4.08611 -8.38892 1.59109 2.00000 0.00000   -1.0745883\n",
      "#@#  4  232  4.81472 -4.08611 -8.38892 1.50333 2.00000 0.00000   -1.0745907\n",
      "#@#  4  239  4.81472 -4.08611 -8.38892 1.50333 0.38197 0.00000   -1.0746135\n",
      "#@#  4  240  4.81472 -4.08611 -8.38892 1.50333 1.14814 0.00000   -1.0747247\n",
      "#@#  4  244  4.81472 -4.08611 -8.38892 1.50333 1.19209 0.00000   -1.0747298\n",
      "#@#  4  253  4.81472 -4.08611 -8.38892 1.50333 1.19209 0.38197   -1.0748018\n",
      "#@#  4  254  4.81472 -4.08611 -8.38892 1.50333 1.19209 0.43756   -1.0748051\n",
      "  powell nthiter 1: fret = -1.074805\n",
      "#@#  4  265  5.19669 -4.08611 -8.38892 1.50333 1.19209 0.43756   -1.0748668\n",
      "#@#  4  266  5.11717 -4.08611 -8.38892 1.50333 1.19209 0.43756   -1.0748727\n",
      "#@#  4  267  5.10717 -4.08611 -8.38892 1.50333 1.19209 0.43756   -1.0748737\n",
      "#@#  4  277  5.10717 -4.16190 -8.38892 1.50333 1.19209 0.43756   -1.0748751\n",
      "#@#  4  288  5.10717 -4.17344 -8.00696 1.50333 1.19209 0.43756   -1.0749029\n",
      "#@#  4  289  5.10717 -4.17344 -8.11559 1.50333 1.19209 0.43756   -1.0749060\n",
      "#@#  4  290  5.10717 -4.17344 -8.09978 1.50333 1.19209 0.43756   -1.0749075\n",
      "#@#  4  299  5.10717 -4.17344 -8.09978 1.39894 1.19209 0.43756   -1.0749296\n",
      "#@#  4  303  5.10717 -4.17344 -8.09978 1.40894 1.19209 0.43756   -1.0749297\n",
      "#@#  4  311  5.10717 -4.17344 -8.09978 1.40894 0.96428 0.43756   -1.0749354\n",
      "#@#  4  312  5.10717 -4.17344 -8.09978 1.40894 1.00193 0.43756   -1.0749359\n",
      "#@#  4  320  5.10717 -4.17344 -8.09978 1.40894 1.00193 0.81953   -1.0749655\n",
      "#@#  4  321  5.10717 -4.17344 -8.09978 1.40894 1.00193 0.72302   -1.0749689\n",
      "#@#  4  322  5.10717 -4.17344 -8.09978 1.40894 1.00193 0.73302   -1.0749718\n",
      "#@#  4  325  5.39961 -4.26077 -7.81065 1.31455 0.81178 1.02847   -1.0749967\n",
      "  powell nthiter 2: fret = -1.074972\n",
      "#@#  4  332  5.34139 -4.17344 -8.09978 1.40894 1.00193 0.73302   -1.0750208\n",
      "#@#  4  334  5.31934 -4.17344 -8.09978 1.40894 1.00193 0.73302   -1.0750209\n",
      "#@#  4  344  5.31934 -4.11550 -8.09978 1.40894 1.00193 0.73302   -1.0750251\n",
      "#@#  4  354  5.31934 -4.11550 -8.08025 1.40894 1.00193 0.73302   -1.0750273\n",
      "#@#  4  356  5.31934 -4.11550 -8.07025 1.40894 1.00193 0.73302   -1.0750297\n",
      "#@#  4  364  5.31934 -4.11550 -8.07025 1.39263 1.00193 0.73302   -1.0750308\n",
      "#@#  4  366  5.31934 -4.11550 -8.07025 1.33482 1.00193 0.73302   -1.0750312\n",
      "#@#  4  377  5.31934 -4.11550 -8.07025 1.33482 0.91988 0.73302   -1.0750325\n",
      "#@#  4  389  5.31934 -4.11550 -8.07025 1.33482 0.91988 0.88265   -1.0750453\n",
      "Powell done niters total = 2\n",
      "OptTimeSec  8.2 sec\n",
      "OptTimeMin  0.14 min\n",
      "nEvals 393\n",
      "Final parameters   5.31934357  -4.11549950  -8.07024860   1.33481693   0.91987813   0.88264996 \n",
      "Final cost   -1.075045376226370\n",
      " \n",
      "\n",
      "---------------------------------\n",
      "mri_coreg utimesec    45.904000\n",
      "mri_coreg stimesec    0.112000\n",
      "mri_coreg ru_maxrss   426844\n",
      "mri_coreg ru_ixrss    0\n",
      "mri_coreg ru_idrss    0\n",
      "mri_coreg ru_isrss    0\n",
      "mri_coreg ru_minflt   126902\n",
      "mri_coreg ru_majflt   0\n",
      "mri_coreg ru_nswap    0\n",
      "mri_coreg ru_inblock  0\n",
      "mri_coreg ru_oublock  0\n",
      "mri_coreg ru_msgsnd   0\n",
      "mri_coreg ru_msgrcv   0\n",
      "mri_coreg ru_nsignals 0\n",
      "mri_coreg ru_nvcsw    47\n",
      "mri_coreg ru_nivcsw   81\n",
      "Final  RefRAS-to-MovRAS\n",
      " 0.99975   0.01540   0.01605   5.31934;\n",
      "-0.01577   0.99960   0.02329  -4.11550;\n",
      "-0.01569  -0.02354   0.99960  -8.07025;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Final  RefVox-to-MovVox\n",
      " 0.49953  -0.00072  -0.02156   2.24036;\n",
      "-0.02075   0.12052  -0.48481   109.52232;\n",
      "-0.00589  -0.48526  -0.12038   88.65955;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Final parameters  5.3193 -4.1155 -8.0702  1.3348  0.9199  0.8826 \n",
      "nhits = 76133 out of 16777216, Percent Overlap:  29.0\n",
      "mri_coreg RunTimeSec 46.0 sec\n",
      "To check run:\n",
      "   tkregisterfv --mov bold/005/tmp.bbregister.27643/template.nii --targ /usr/local/freesurfer/subjects/pBrain/mri/brainmask.mgz --reg bold/005/tmp.bbregister.27643/mri_coreg.lta --s pBrain --surfs \n",
      "\n",
      "mri_coreg done\n",
      "\n",
      "mri_segreg --mov bold/005/tmp.bbregister.27643/template.nii --init-reg bold/005/tmp.bbregister.27643/reg.init.dat --out-reg bold/005/tmp.bbregister.27643/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/hands/Sess01\n",
      "mri_segreg --mov bold/005/tmp.bbregister.27643/template.nii --init-reg bold/005/tmp.bbregister.27643/reg.init.dat --out-reg bold/005/tmp.bbregister.27643/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "movvol bold/005/tmp.bbregister.27643/template.nii\n",
      "regfile bold/005/tmp.bbregister.27643/reg.init.dat\n",
      "subject pBrain\n",
      "dof 6\n",
      "outregfile bold/005/tmp.bbregister.27643/bbr.pass1.dat\n",
      "UseMask 0\n",
      "UseLH 1\n",
      "UseRH 1\n",
      "nsubsamp 100\n",
      "PenaltySign  -1\n",
      "PenaltySlope 0.500000\n",
      "PenaltyCenter 0.000000\n",
      "surfname white\n",
      "GMProjFrac 0.500000\n",
      "WMProjAbs 2.000000\n",
      "lhcostfile (null)\n",
      "rhcostfile (null)\n",
      "interp  trilinear (1)\n",
      "frame  0\n",
      "TolPowell 0.000100\n",
      "nMaxItersPowell 36\n",
      "n1dmin  3\n",
      "Profile   0\n",
      "Gdiag_no  -1\n",
      "AddNoise  0 (0)\n",
      "SynthSeed 1511683397\n",
      "TransRandMax 0.000000\n",
      "RotRandMax 0.000000\n",
      "Translations 0.000000 0.000000 0.000000\n",
      "Rotations   0.000000 0.000000 0.000000\n",
      "Input reg\n",
      " 0.99907   0.04311  -0.00144   1.34099;\n",
      " 0.01179  -0.24077   0.97051  -19.23314;\n",
      "-0.04150   0.96963   0.24105   7.52451;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Loading mov\n",
      "Projecting LH Surfs\n",
      "Loading lh.white surf\n",
      "Loading lh.thickness for GM\n",
      "GM Proj: 1 0.500000 2.000000\n",
      "WM Proj: 0 0.500000 2.000000\n",
      "Projecting RH Surfs\n",
      "Loading rh.white surf\n",
      "Loading rh.thickness for GM\n",
      "Projecting RH Surfs\n",
      "Using lh.cortex.label\n",
      "Using rh.cortex.label\n",
      "Computing relative cost\n",
      " 0  -25.0 -25.0 -25.0   0.972294\n",
      " 1  -25.0 -25.0  25.0   1.013251\n",
      " 2  -25.0  25.0 -25.0   1.029777\n",
      " 3  -25.0  25.0  25.0   0.996949\n",
      " 4   25.0 -25.0 -25.0   1.057780\n",
      " 5   25.0 -25.0  25.0   1.036454\n",
      " 6   25.0  25.0 -25.0   1.058518\n",
      " 7   25.0  25.0  25.0   1.060795\n",
      "REL:  8  0.563638    8.225817  1.028227 rel = 0.548165 \n",
      "Initial costs ----------------\n",
      "Number of surface hits 1609\n",
      "WM  Intensity   772.3745 +/- 106.8696\n",
      "Ctx Intensity   827.5119 +/- 154.3245\n",
      "Pct Contrast      5.4874 +/-  21.5555\n",
      "Cost   0.5636\n",
      "RelCost   0.5482\n",
      "\n",
      "------------------------------------\n",
      "Brute force preopt -4 4 4, n = 729\n",
      "     0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      1.0690   1.0690  0.0\n",
      "     1  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   0.0000      1.0635   1.0635  0.0\n",
      "     3  -4.0000  -4.0000  -4.0000  -4.0000   0.0000  -4.0000      1.0471   1.0471  0.0\n",
      "     4  -4.0000  -4.0000  -4.0000  -4.0000   0.0000   0.0000      1.0358   1.0358  0.0\n",
      "     6  -4.0000  -4.0000  -4.0000  -4.0000   4.0000  -4.0000      0.9520   0.9520  0.0\n",
      "    15  -4.0000  -4.0000  -4.0000   0.0000   4.0000  -4.0000      0.9316   0.9316  0.0\n",
      "    43  -4.0000  -4.0000   0.0000   0.0000   4.0000   0.0000      0.9316   0.9316  0.0\n",
      "    45  -4.0000  -4.0000   0.0000   4.0000  -4.0000  -4.0000      0.8915   0.8915  0.0\n",
      "   106  -4.0000   0.0000  -4.0000   4.0000   4.0000   0.0000      0.8764   0.8764  0.0\n",
      "   117  -4.0000   0.0000   0.0000   0.0000  -4.0000  -4.0000      0.8753   0.8753  0.0\n",
      "   118  -4.0000   0.0000   0.0000   0.0000  -4.0000   0.0000      0.8554   0.8554  0.0\n",
      "   274   0.0000  -4.0000   0.0000  -4.0000   0.0000   0.0000      0.8346   0.8346  0.0\n",
      "   292   0.0000  -4.0000   0.0000   4.0000   0.0000   0.0000      0.7879   0.7879  0.0\n",
      "   337   0.0000   0.0000  -4.0000   0.0000   0.0000   0.0000      0.7300   0.7300  0.0\n",
      "   346   0.0000   0.0000  -4.0000   4.0000   0.0000   0.0000      0.7167   0.7167  0.0\n",
      "   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.5636   0.5636  0.0\n",
      "Brute Force --------------------------\n",
      "Min cost was 0.563638\n",
      "Number of iterations   729\n",
      "Search time 0.602000 sec\n",
      "Parameters at best (transmm, rotdeg)\n",
      "  0.000   0.000   0.000  0.000  0.000  0.000 \n",
      "--------------------------------------------\n",
      "\n",
      "Starting Powell Minimization\n",
      "Init Powel Params dof = 6\n",
      "0 0\n",
      "1 0\n",
      "2 0\n",
      "3 0\n",
      "4 0\n",
      "5 0\n",
      "fs_powell::minimize\n",
      "  nparams 6\n",
      "  maxfev 36\n",
      "  ftol   0.000100\n",
      "  linmin_xtol_   0.001000\n",
      "  powell nthiter 0: fret = 0.563638\n",
      "   6  0.382  0.000  0.000  0.000  0.000  0.000   0.5582658620\n",
      "   7  0.344  0.000  0.000  0.000  0.000  0.000   0.5576989104\n",
      "   8  0.274  0.000  0.000  0.000  0.000  0.000   0.5575807312\n",
      "  10  0.302  0.000  0.000  0.000  0.000  0.000   0.5574341943\n",
      "  12  0.301  0.000  0.000  0.000  0.000  0.000   0.5574335007\n",
      "  14  0.300  0.000  0.000  0.000  0.000  0.000   0.5574333142\n",
      "  20  0.300 -0.618  0.000  0.000  0.000  0.000   0.5468261399\n",
      "  25  0.300 -0.581  0.000  0.000  0.000  0.000   0.5467094825\n",
      "  27  0.300 -0.561  0.000  0.000  0.000  0.000   0.5465739277\n",
      "  30  0.300 -0.556  0.000  0.000  0.000  0.000   0.5465510723\n",
      "  33  0.300 -0.555  0.000  0.000  0.000  0.000   0.5465458821\n",
      "  36  0.300 -0.555 -1.618  0.000  0.000  0.000   0.4913494739\n",
      "  37  0.300 -0.555 -1.378  0.000  0.000  0.000   0.4860695356\n",
      "  42  0.300 -0.555 -1.314  0.000  0.000  0.000   0.4859927467\n",
      "  44  0.300 -0.555 -1.324  0.000  0.000  0.000   0.4859868054\n",
      "  45  0.300 -0.555 -1.328  0.000  0.000  0.000   0.4859693383\n",
      "  46  0.300 -0.555 -1.347  0.000  0.000  0.000   0.4859161860\n",
      "  48  0.300 -0.555 -1.350  0.000  0.000  0.000   0.4859138044\n",
      "  49  0.300 -0.555 -1.351  0.000  0.000  0.000   0.4859129301\n",
      "  50  0.300 -0.555 -1.353  0.000  0.000  0.000   0.4859118814\n",
      "  54  0.300 -0.555 -1.353  1.000  0.000  0.000   0.4315456395\n",
      "  59  0.300 -0.555 -1.353  1.019  0.000  0.000   0.4308233508\n",
      "  60  0.300 -0.555 -1.353  1.248  0.000  0.000   0.4288236818\n",
      "  61  0.300 -0.555 -1.353  1.169  0.000  0.000   0.4266700210\n",
      "  64  0.300 -0.555 -1.353  1.167  0.000  0.000   0.4266583117\n",
      "  74  0.300 -0.555 -1.353  1.167 -0.279  0.000   0.4197752567\n",
      "  75  0.300 -0.555 -1.353  1.167 -0.278  0.000   0.4197684427\n",
      "  76  0.300 -0.555 -1.353  1.167 -0.252  0.000   0.4197049912\n",
      "  78  0.300 -0.555 -1.353  1.167 -0.255  0.000   0.4197028710\n",
      "  87  0.300 -0.555 -1.353  1.167 -0.255 -0.166   0.4174022758\n",
      "  88  0.300 -0.555 -1.353  1.167 -0.255 -0.220   0.4171172997\n",
      "  89  0.300 -0.555 -1.353  1.167 -0.255 -0.261   0.4169591894\n",
      "  94  0.300 -0.555 -1.353  1.167 -0.255 -0.260   0.4169589975\n",
      "  powell nthiter 1: fret = 0.416959\n",
      " 103  0.038 -0.555 -1.353  1.167 -0.255 -0.260   0.4106814097\n",
      " 105  0.061 -0.555 -1.353  1.167 -0.255 -0.260   0.4106332115\n",
      " 107  0.057 -0.555 -1.353  1.167 -0.255 -0.260   0.4106322931\n",
      " 108  0.058 -0.555 -1.353  1.167 -0.255 -0.260   0.4106322259\n",
      " 114  0.058 -1.173 -1.353  1.167 -0.255 -0.260   0.3817312908\n",
      " 118  0.058 -1.106 -1.353  1.167 -0.255 -0.260   0.3793619857\n",
      " 120  0.058 -1.097 -1.353  1.167 -0.255 -0.260   0.3792676143\n",
      " 131  0.058 -1.097 -1.561  1.167 -0.255 -0.260   0.3755357623\n",
      " 133  0.058 -1.097 -1.503  1.167 -0.255 -0.260   0.3753039219\n",
      " 135  0.058 -1.097 -1.526  1.167 -0.255 -0.260   0.3751672845\n",
      " 144  0.058 -1.097 -1.526  1.272 -0.255 -0.260   0.3751656248\n",
      " 145  0.058 -1.097 -1.526  1.220 -0.255 -0.260   0.3750042596\n",
      " 146  0.058 -1.097 -1.526  1.221 -0.255 -0.260   0.3750007412\n",
      " 148  0.058 -1.097 -1.526  1.226 -0.255 -0.260   0.3749866993\n",
      " 151  0.058 -1.097 -1.526  1.227 -0.255 -0.260   0.3749838217\n",
      " 158  0.058 -1.097 -1.526  1.227 -0.391 -0.260   0.3723817289\n",
      " 160  0.058 -1.097 -1.526  1.227 -0.355 -0.260   0.3720466484\n",
      " 163  0.058 -1.097 -1.526  1.227 -0.356 -0.260   0.3720465537\n",
      " 171  0.058 -1.097 -1.526  1.227 -0.356 -0.192   0.3705759971\n",
      " 172  0.058 -1.097 -1.526  1.227 -0.356 -0.131   0.3700085980\n",
      " 173  0.058 -1.097 -1.526  1.227 -0.356 -0.111   0.3699569354\n",
      " 175  0.058 -1.097 -1.526  1.227 -0.356 -0.109   0.3699564799\n",
      " 176  0.058 -1.097 -1.526  1.227 -0.356 -0.110   0.3699563694\n",
      "  powell nthiter 2: fret = 0.369956\n",
      " 185  0.039 -1.097 -1.526  1.227 -0.356 -0.110   0.3697147513\n",
      " 186  0.030 -1.097 -1.526  1.227 -0.356 -0.110   0.3696889227\n",
      " 195  0.030 -1.195 -1.526  1.227 -0.356 -0.110   0.3696262711\n",
      " 196  0.030 -1.148 -1.526  1.227 -0.356 -0.110   0.3692209541\n",
      " 197  0.030 -1.147 -1.526  1.227 -0.356 -0.110   0.3692168629\n",
      " 199  0.030 -1.139 -1.526  1.227 -0.356 -0.110   0.3692009457\n",
      " 211  0.030 -1.139 -1.529  1.227 -0.356 -0.110   0.3692004071\n",
      " 214  0.030 -1.139 -1.528  1.227 -0.356 -0.110   0.3692001722\n",
      " 222  0.030 -1.139 -1.528  1.334 -0.356 -0.110   0.3665935742\n",
      " 223  0.030 -1.139 -1.528  1.359 -0.356 -0.110   0.3664043382\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " 224  0.030 -1.139 -1.528  1.377 -0.356 -0.110   0.3663131351\n",
      " 227  0.030 -1.139 -1.528  1.384 -0.356 -0.110   0.3662994817\n",
      " 229  0.030 -1.139 -1.528  1.385 -0.356 -0.110   0.3662991468\n",
      " 237  0.030 -1.139 -1.528  1.385 -0.437 -0.110   0.3649163469\n",
      " 239  0.030 -1.139 -1.528  1.385 -0.428 -0.110   0.3648993093\n",
      "  powell nthiter 3: fret = 0.364899\n",
      " 260  0.006 -1.139 -1.528  1.385 -0.428 -0.110   0.3646479987\n",
      " 261 -0.001 -1.139 -1.528  1.385 -0.428 -0.110   0.3646428661\n",
      " 262  0.001 -1.139 -1.528  1.385 -0.428 -0.110   0.3646422311\n",
      " 272  0.001 -1.156 -1.528  1.385 -0.428 -0.110   0.3644759289\n",
      " 273  0.001 -1.157 -1.528  1.385 -0.428 -0.110   0.3644700073\n",
      " 274  0.001 -1.162 -1.528  1.385 -0.428 -0.110   0.3644664203\n",
      " 275  0.001 -1.180 -1.528  1.385 -0.428 -0.110   0.3643778736\n",
      " 277  0.001 -1.173 -1.528  1.385 -0.428 -0.110   0.3642990994\n",
      " 278  0.001 -1.172 -1.528  1.385 -0.428 -0.110   0.3642907620\n",
      " 279  0.001 -1.168 -1.528  1.385 -0.428 -0.110   0.3642637397\n",
      " 280  0.001 -1.165 -1.528  1.385 -0.428 -0.110   0.3642523182\n",
      " 281  0.001 -1.164 -1.528  1.385 -0.428 -0.110   0.3642476131\n",
      " 282  0.001 -1.163 -1.528  1.385 -0.428 -0.110   0.3642454662\n",
      " 290  0.001 -1.163 -1.544  1.385 -0.428 -0.110   0.3642363093\n",
      " 291  0.001 -1.163 -1.538  1.385 -0.428 -0.110   0.3642234131\n",
      " 292  0.001 -1.163 -1.537  1.385 -0.428 -0.110   0.3642223804\n",
      " 293  0.001 -1.163 -1.534  1.385 -0.428 -0.110   0.3642222182\n",
      " 295  0.001 -1.163 -1.535  1.385 -0.428 -0.110   0.3642215886\n",
      " 304  0.001 -1.163 -1.535  1.382 -0.428 -0.110   0.3642207504\n",
      " 306  0.001 -1.163 -1.535  1.383 -0.428 -0.110   0.3642206341\n",
      " 314  0.001 -1.163 -1.535  1.383 -0.440 -0.110   0.3641710454\n",
      " 315  0.001 -1.163 -1.535  1.383 -0.442 -0.110   0.3641709216\n",
      " 325  0.001 -1.163 -1.535  1.383 -0.442 -0.111   0.3641675870\n",
      " 327  0.001 -1.163 -1.535  1.383 -0.442 -0.116   0.3641560687\n",
      "  powell nthiter 4: fret = 0.364156\n",
      " 339 -0.003 -1.163 -1.535  1.383 -0.442 -0.116   0.3641536650\n",
      " 340 -0.002 -1.163 -1.535  1.383 -0.442 -0.116   0.3641533201\n",
      " 364 -0.002 -1.163 -1.536  1.383 -0.442 -0.116   0.3641524051\n",
      " 365 -0.002 -1.163 -1.537  1.383 -0.442 -0.116   0.3641514184\n",
      " 367 -0.002 -1.163 -1.538  1.383 -0.442 -0.116   0.3641512512\n",
      " 387 -0.002 -1.163 -1.538  1.383 -0.445 -0.116   0.3641503410\n",
      " 390 -0.002 -1.163 -1.538  1.383 -0.444 -0.116   0.3641499245\n",
      "Powell done niters = 4\n",
      "Computing relative cost\n",
      " 0  -25.0 -25.0 -25.0   1.026539\n",
      " 1  -25.0 -25.0  25.0   1.013429\n",
      " 2  -25.0  25.0 -25.0   1.012189\n",
      " 3  -25.0  25.0  25.0   1.017259\n",
      " 4   25.0 -25.0 -25.0   1.019175\n",
      " 5   25.0 -25.0  25.0   1.058407\n",
      " 6   25.0  25.0 -25.0   1.114943\n",
      " 7   25.0  25.0  25.0   1.022345\n",
      "REL:  8  0.364150    8.284285  1.035536 rel = 0.351654 \n",
      "Number of iterations     4\n",
      "Min cost was 0.364150\n",
      "Number of FunctionCalls   406\n",
      "TolPowell 0.000100\n",
      "nMaxItersPowell 36\n",
      "OptimizationTime 0.333000 sec\n",
      "Parameters at optimum (transmm) -0.00153 -1.16296 -1.53836\n",
      "Parameters at optimum (rotdeg)  1.38325 -0.44372 -0.11596 \n",
      "Final costs ----------------\n",
      "Number of surface hits 1637\n",
      "WM  Intensity   746.9640 +/- 115.8444\n",
      "Ctx Intensity   829.9575 +/- 167.5774\n",
      "Pct Contrast      8.8686 +/-  22.3589\n",
      "Cost   0.3641\n",
      "RelCost   0.5482\n",
      "Reg at min cost was \n",
      " 0.99938   0.03512  -0.00153   1.24547;\n",
      " 0.01076  -0.26417   0.96442  -20.57470;\n",
      "-0.03346   0.96384   0.26439   5.52984;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Writing optimal reg to bold/005/tmp.bbregister.27643/bbr.pass1.dat, type = 14 \n",
      "Original Reg \n",
      " 0.99907   0.04311  -0.00144   1.34099;\n",
      " 0.01179  -0.24077   0.97051  -19.23314;\n",
      "-0.04150   0.96963   0.24105   7.52451;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Original Reg - Optimal Reg\n",
      "-0.00031   0.00800   0.00010   0.09552;\n",
      " 0.00102   0.02341   0.00610   1.34156;\n",
      "-0.00803   0.00579  -0.02334   1.99467;\n",
      " 0.00000   0.00000   0.00000   0.00000;\n",
      "\n",
      "Computing change in lh position\n",
      "LH rmsDiffMean 1.770248\n",
      "Computing change in rh position\n",
      "Surface-RMS-Diff-mm 1.681189 0.639269 3.310816\n",
      "mri_segreg done\n",
      "mri_segreg --mov bold/005/tmp.bbregister.27643/template.nii --init-reg bold/005/tmp.bbregister.27643/bbr.pass1.dat --out-reg bold/005/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/005/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/005/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/005/tmp.bbregister.27643/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5\n",
      "$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/hands/Sess01\n",
      "mri_segreg --mov bold/005/tmp.bbregister.27643/template.nii --init-reg bold/005/tmp.bbregister.27643/bbr.pass1.dat --out-reg bold/005/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/005/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/005/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/005/tmp.bbregister.27643/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "movvol bold/005/tmp.bbregister.27643/template.nii\n",
      "regfile bold/005/tmp.bbregister.27643/bbr.pass1.dat\n",
      "subject pBrain\n",
      "dof 6\n",
      "outregfile bold/005/register.dof6.dat\n",
      "UseMask 0\n",
      "UseLH 1\n",
      "UseRH 1\n",
      "nsubsamp 1\n",
      "PenaltySign  -1\n",
      "PenaltySlope 0.500000\n",
      "PenaltyCenter 0.000000\n",
      "surfname white\n",
      "GMProjFrac 0.500000\n",
      "WMProjAbs 2.000000\n",
      "lhcostfile (null)\n",
      "rhcostfile (null)\n",
      "interp  trilinear (1)\n",
      "frame  0\n",
      "TolPowell 0.000000\n",
      "nMaxItersPowell 36\n",
      "n1dmin  3\n",
      "Profile   0\n",
      "Gdiag_no  -1\n",
      "AddNoise  0 (0)\n",
      "SynthSeed 1511872260\n",
      "TransRandMax 0.000000\n",
      "RotRandMax 0.000000\n",
      "Translations 0.000000 0.000000 0.000000\n",
      "Rotations   0.000000 0.000000 0.000000\n",
      "Input reg\n",
      " 0.99938   0.03512  -0.00153   1.24547;\n",
      " 0.01076  -0.26417   0.96442  -20.57470;\n",
      "-0.03346   0.96384   0.26439   5.52984;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Loading mov\n",
      "Projecting LH Surfs\n",
      "Loading lh.white surf\n",
      "Loading lh.thickness for GM\n",
      "GM Proj: 1 0.500000 2.000000\n",
      "WM Proj: 0 0.500000 2.000000\n",
      "Projecting RH Surfs\n",
      "Loading rh.white surf\n",
      "Loading rh.thickness for GM\n",
      "Projecting RH Surfs\n",
      "Using lh.cortex.label\n",
      "Using rh.cortex.label\n",
      "Computing relative cost\n",
      " 0  -25.0 -25.0 -25.0   1.023146\n",
      " 1  -25.0 -25.0  25.0   1.010952\n",
      " 2  -25.0  25.0 -25.0   1.036815\n",
      " 3  -25.0  25.0  25.0   1.021077\n",
      " 4   25.0 -25.0 -25.0   1.018669\n",
      " 5   25.0 -25.0  25.0   1.030663\n",
      " 6   25.0  25.0 -25.0   1.039424\n",
      " 7   25.0  25.0  25.0   1.018707\n",
      "REL:  8  0.363373    8.199453  1.024932 rel = 0.354534 \n",
      "Initial costs ----------------\n",
      "Number of surface hits 163468\n",
      "WM  Intensity   747.2617 +/- 118.6361\n",
      "Ctx Intensity   832.4796 +/- 166.8274\n",
      "Pct Contrast      9.2387 +/-  21.9855\n",
      "Cost   0.3634\n",
      "RelCost   0.3545\n",
      "\n",
      "------------------------------------\n",
      "Brute force preopt -0.1 0.1 0.1, n = 729\n",
      "     0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.3770   0.3770  0.0\n",
      "     1  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000   0.0000      0.3745   0.3745  0.0\n",
      "     2  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000   0.1000      0.3740   0.3740  0.0\n",
      "     4  -0.1000  -0.1000  -0.1000  -0.1000   0.0000   0.0000      0.3734   0.3734  0.0\n",
      "     5  -0.1000  -0.1000  -0.1000  -0.1000   0.0000   0.1000      0.3731   0.3731  0.0\n",
      "    10  -0.1000  -0.1000  -0.1000   0.0000  -0.1000   0.0000      0.3724   0.3724  0.0\n",
      "    13  -0.1000  -0.1000  -0.1000   0.0000   0.0000   0.0000      0.3723   0.3723  0.0\n",
      "    18  -0.1000  -0.1000  -0.1000   0.1000  -0.1000  -0.1000      0.3722   0.3722  0.0\n",
      "    21  -0.1000  -0.1000  -0.1000   0.1000   0.0000  -0.1000      0.3719   0.3719  0.0\n",
      "    31  -0.1000  -0.1000   0.0000  -0.1000   0.0000   0.0000      0.3718   0.3718  0.0\n",
      "    32  -0.1000  -0.1000   0.0000  -0.1000   0.0000   0.1000      0.3714   0.3714  0.0\n",
      "    37  -0.1000  -0.1000   0.0000   0.0000  -0.1000   0.0000      0.3706   0.3706  0.0\n",
      "    40  -0.1000  -0.1000   0.0000   0.0000   0.0000   0.0000      0.3700   0.3700  0.0\n",
      "    82  -0.1000   0.0000  -0.1000  -0.1000  -0.1000   0.0000      0.3685   0.3685  0.0\n",
      "    91  -0.1000   0.0000  -0.1000   0.0000  -0.1000   0.0000      0.3672   0.3672  0.0\n",
      "    94  -0.1000   0.0000  -0.1000   0.0000   0.0000   0.0000      0.3668   0.3668  0.0\n",
      "   121  -0.1000   0.0000   0.0000   0.0000   0.0000   0.0000      0.3664   0.3664  0.0\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "   337   0.0000   0.0000  -0.1000   0.0000   0.0000   0.0000      0.3657   0.3657  0.0\n",
      "   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.3641   0.3641  0.0\n",
      "Brute Force --------------------------\n",
      "Min cost was 0.364150\n",
      "Number of iterations   729\n",
      "Search time 0.599000 sec\n",
      "Parameters at best (transmm, rotdeg)\n",
      "  0.000   0.000   0.000  0.000  0.000  0.000 \n",
      "--------------------------------------------\n",
      "\n",
      "Starting Powell Minimization\n",
      "Init Powel Params dof = 6\n",
      "0 0\n",
      "1 0\n",
      "2 0\n",
      "3 0\n",
      "4 0\n",
      "5 0\n",
      "fs_powell::minimize\n",
      "  nparams 6\n",
      "  maxfev 36\n",
      "  ftol   0.000000\n",
      "  linmin_xtol_   0.001000\n",
      "  powell nthiter 0: fret = 0.363373\n",
      "   7  0.043  0.000  0.000  0.000  0.000  0.000   0.3631923066\n",
      "   8  0.048  0.000  0.000  0.000  0.000  0.000   0.3631885970\n",
      "   9  0.052  0.000  0.000  0.000  0.000  0.000   0.3631861754\n",
      "  11  0.056  0.000  0.000  0.000  0.000  0.000   0.3631850564\n",
      "  21  0.056  0.150  0.000  0.000  0.000  0.000   0.3614438623\n",
      "  22  0.056  0.144  0.000  0.000  0.000  0.000   0.3614282638\n",
      "  23  0.056  0.133  0.000  0.000  0.000  0.000   0.3614184815\n",
      "  27  0.056  0.124  0.000  0.000  0.000  0.000   0.3614096225\n",
      "  28  0.056  0.125  0.000  0.000  0.000  0.000   0.3614083972\n",
      "  29  0.056  0.127  0.000  0.000  0.000  0.000   0.3614072796\n",
      "  30  0.056  0.129  0.000  0.000  0.000  0.000   0.3614042947\n",
      "  39  0.056  0.129 -0.143  0.000  0.000  0.000   0.3604629004\n",
      "  40  0.056  0.129 -0.124  0.000  0.000  0.000   0.3604142601\n",
      "  41  0.056  0.129 -0.116  0.000  0.000  0.000   0.3604079914\n",
      "  50  0.056  0.129 -0.116 -0.039  0.000  0.000   0.3603784770\n",
      "  55  0.056  0.129 -0.116 -0.032  0.000  0.000   0.3603741650\n",
      "  58  0.056  0.129 -0.116 -0.031  0.000  0.000   0.3603732881\n",
      "  65  0.056  0.129 -0.116 -0.031  0.047  0.000   0.3600263861\n",
      "  66  0.056  0.129 -0.116 -0.031  0.065  0.000   0.3600031900\n",
      "  67  0.056  0.129 -0.116 -0.031  0.063  0.000   0.3600025518\n",
      "  76  0.056  0.129 -0.116 -0.031  0.063  0.140   0.3591235241\n",
      "  78  0.056  0.129 -0.116 -0.031  0.063  0.127   0.3591169636\n",
      "  80  0.056  0.129 -0.116 -0.031  0.063  0.130   0.3591139801\n",
      "  82  0.056  0.129 -0.116 -0.031  0.063  0.129   0.3591134220\n",
      "  powell nthiter 1: fret = 0.359113\n",
      "  91  0.105  0.129 -0.116 -0.031  0.063  0.129   0.3589021555\n",
      "  92  0.108  0.129 -0.116 -0.031  0.063  0.129   0.3588999109\n",
      "  93  0.111  0.129 -0.116 -0.031  0.063  0.129   0.3588993192\n",
      " 103  0.111  0.143 -0.116 -0.031  0.063  0.129   0.3588790004\n",
      " 105  0.111  0.137 -0.116 -0.031  0.063  0.129   0.3588783113\n",
      " 107  0.111  0.140 -0.116 -0.031  0.063  0.129   0.3588720305\n",
      " 117  0.111  0.140 -0.102 -0.031  0.063  0.129   0.3588546041\n",
      " 118  0.111  0.140 -0.098 -0.031  0.063  0.129   0.3588540353\n",
      " 119  0.111  0.140 -0.099 -0.031  0.063  0.129   0.3588539534\n",
      " 143  0.111  0.140 -0.099 -0.031  0.055  0.129   0.3588514436\n",
      " 145  0.111  0.140 -0.099 -0.031  0.057  0.129   0.3588513096\n",
      " 146  0.111  0.140 -0.099 -0.031  0.058  0.129   0.3588511003\n",
      " 154  0.111  0.140 -0.099 -0.031  0.058  0.163   0.3588258387\n",
      " 157  0.111  0.140 -0.099 -0.031  0.058  0.183   0.3588096660\n",
      " 160  0.111  0.140 -0.099 -0.031  0.058  0.175   0.3587972231\n",
      "  powell nthiter 2: fret = 0.358797\n",
      " 171  0.114  0.140 -0.099 -0.031  0.058  0.175   0.3587935656\n",
      " 172  0.120  0.140 -0.099 -0.031  0.058  0.175   0.3587912493\n",
      " 173  0.121  0.140 -0.099 -0.031  0.058  0.175   0.3587912193\n",
      " 198  0.121  0.140 -0.098 -0.031  0.058  0.175   0.3587910060\n",
      "  powell nthiter 3: fret = 0.358791\n",
      "Powell done niters = 3\n",
      "Computing relative cost\n",
      " 0  -25.0 -25.0 -25.0   1.022950\n",
      " 1  -25.0 -25.0  25.0   1.009761\n",
      " 2  -25.0  25.0 -25.0   1.036705\n",
      " 3  -25.0  25.0  25.0   1.022337\n",
      " 4   25.0 -25.0 -25.0   1.018664\n",
      " 5   25.0 -25.0  25.0   1.030867\n",
      " 6   25.0  25.0 -25.0   1.040351\n",
      " 7   25.0  25.0  25.0   1.018918\n",
      "REL:  8  0.358791    8.200553  1.025069 rel = 0.350016 \n",
      "Number of iterations     3\n",
      "Min cost was 0.358791\n",
      "Number of FunctionCalls   298\n",
      "TolPowell 0.000000\n",
      "nMaxItersPowell 36\n",
      "OptimizationTime 11.853000 sec\n",
      "Parameters at optimum (transmm)  0.12053  0.13970 -0.09763\n",
      "Parameters at optimum (rotdeg) -0.03091  0.05834  0.17542 \n",
      "Final costs ----------------\n",
      "Number of surface hits 163051\n",
      "WM  Intensity   747.6133 +/- 116.8898\n",
      "Ctx Intensity   833.9871 +/- 165.5010\n",
      "Pct Contrast      9.3880 +/-  21.9105\n",
      "Cost   0.3588\n",
      "RelCost   0.3545\n",
      "Reg at min cost was \n",
      " 0.99931   0.03690  -0.00422   1.43462;\n",
      " 0.01380  -0.26354   0.96455  -20.42809;\n",
      "-0.03448   0.96394   0.26387   5.44204;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Writing optimal reg to bold/005/register.dof6.dat, type = 14 \n",
      "Original Reg \n",
      " 0.99938   0.03512  -0.00153   1.24547;\n",
      " 0.01076  -0.26417   0.96442  -20.57470;\n",
      "-0.03346   0.96384   0.26439   5.52984;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Original Reg - Optimal Reg\n",
      " 0.00007  -0.00179   0.00268  -0.18914;\n",
      "-0.00304  -0.00063  -0.00013  -0.14661;\n",
      " 0.00102  -0.00011   0.00052   0.08780;\n",
      " 0.00000   0.00000   0.00000   0.00000;\n",
      "\n",
      "Computing change in lh position\n",
      "LH rmsDiffMean 0.140609\n",
      "Computing change in rh position\n",
      "Surface-RMS-Diff-mm 0.204989 0.081213 0.385722\n",
      "mri_segreg done\n",
      "MinCost: 0.358791 747.613278 833.987104 9.387982 \n",
      "tkregister2_cmdl --mov bold/005/template.nii.gz --reg bold/005/register.dof6.dat --noedit --ltaout bold/005/register.dof6.lta\n",
      "tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl\n",
      "INFO: no target volume specified, assuming FreeSurfer orig volume.\n",
      "target  volume orig\n",
      "movable volume bold/005/template.nii.gz\n",
      "reg file       bold/005/register.dof6.dat\n",
      "LoadVol        0\n",
      "ZeroCRAS       0\n",
      "$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $\n",
      "Diagnostic Level -1\n",
      "---- Input registration matrix --------\n",
      " 0.99931   0.03690  -0.00422   1.43462;\n",
      " 0.01380  -0.26354   0.96455  -20.42809;\n",
      "-0.03448   0.96394   0.26387   5.44204;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "float2int = 0\n",
      "---------------------------------------\n",
      "INFO: loading target /usr/local/freesurfer/subjects/pBrain/mri/orig.mgz\n",
      "Ttarg: --------------------\n",
      "-1.00000   0.00000   0.00000   128.00000;\n",
      " 0.00000   0.00000   1.00000  -128.00000;\n",
      " 0.00000  -1.00000   0.00000   128.00000;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "INFO: loading movable bold/005/template.nii.gz\n",
      "Tmov: --------------------\n",
      "-2.00000   0.00000   0.00000   128.00000;\n",
      " 0.00000   0.00000   2.00000  -40.00000;\n",
      " 0.00000  -2.00000   0.00000   128.00000;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "mkheaderreg = 0, float2int = 0\n",
      "---- Input registration matrix --------\n",
      " 0.99931   0.03690  -0.00422   1.43462;\n",
      " 0.01380  -0.26354   0.96455  -20.42809;\n",
      "-0.03448   0.96394   0.26387   5.44204;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Determinant -1\n",
      "subject = pBrain\n",
      "RegMat ---------------------------\n",
      " 0.99931   0.03690  -0.00422   1.43462;\n",
      " 0.01380  -0.26354   0.96455  -20.42809;\n",
      "-0.03448   0.96394   0.26387   5.44204;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "Cleaning up\n",
      " \n",
      "Started at Fri Nov 24 13:07:04 CET 2017 \n",
      "Ended   at Fri Nov 24 13:08:11 CET 2017\n",
      "BBR-Run-Time-Sec 67\n",
      " \n",
      "bbregister Done\n",
      "To check results, run:\n",
      "tkregisterfv --mov bold/005/template.nii.gz --reg bold/005/register.dof6.lta --surfs \n",
      " \n",
      "Fri Nov 24 13:08:11 CET 2017\n",
      "register-sess completed \n",
      "Sess01 Mask ------------------------\n",
      "mkbrainmask-sess -maskstem brain -fsd bold -s Sess01 -d /data/martin/prosopagnosia/hands -per-run -update\n",
      "------------------------------------------------\n",
      "/data/martin/prosopagnosia/hands/Sess01 \n",
      "Fri Nov 24 13:08:11 CET 2017\n",
      "mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -reg /data/martin/prosopagnosia/hands/Sess01/bold/register.dof6.lta -ndil 1 -nerode 0\n",
      "Fri Nov 24 13:08:11 CET 2017\n",
      "\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/hands/Sess01/bold\n",
      "/usr/local/freesurfer/fsfast/bin/mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -reg /data/martin/prosopagnosia/hands/Sess01/bold/register.dof6.lta -ndil 1 -nerode 0\n",
      "\n",
      "freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c\n",
      "$Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "mri_vol2vol --mov template.nii.gz --reg /data/martin/prosopagnosia/hands/Sess01/bold/register.dof6.lta --inv --interp nearest --o masks/brain.nii.gz --targ /usr/local/freesurfer/subjects/pBrain/mri/aparc+aseg.mgz\n",
      "regio_read_register: loading lta\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "Matrix from regfile:\n",
      " 0.99924   0.03876  -0.00310   1.37698;\n",
      " 0.01321  -0.26354   0.96456  -20.60455;\n",
      "-0.03657   0.96387   0.26385   5.40788;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "movvol template.nii.gz\n",
      "targvol /usr/local/freesurfer/subjects/pBrain/mri/aparc+aseg.mgz\n",
      "outvol masks/brain.nii.gz\n",
      "regfile /data/martin/prosopagnosia/hands/Sess01/bold/register.dof6.lta\n",
      "invert 1\n",
      "tal    0\n",
      "talres 2\n",
      "regheader 0\n",
      "noresample 0\n",
      "interp  nearest (0)\n",
      "precision  float (3)\n",
      "Gdiag_no  -1\n",
      "Synth      0\n",
      "SynthSeed  1511713400\n",
      "\n",
      "Invert!\n",
      "Inverting registration\n",
      "\n",
      "Final tkRAS-to-tkRAS Matrix is:\n",
      " 0.99924   0.01321  -0.03657  -0.90591;\n",
      " 0.03876  -0.26354   0.96387  -10.69599;\n",
      "-0.00310   0.96456   0.26385   18.45166;\n",
      "-0.00000  -0.00000  -0.00000   1.00000;\n",
      "\n",
      "\n",
      "Vox2Vox Matrix is:\n",
      " 1.99849  -0.07315  -0.02643   6.21279;\n",
      "-0.00619   0.52771  -1.92912   114.75374;\n",
      "-0.07753  -1.92774  -0.52708   256.18271;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Resampling\n",
      "Output registration matrix is identity\n",
      "\n",
      "mri_vol2vol done\n",
      "mri_binarize --i masks/brain.nii.gz --o masks/brain.nii.gz --min 0.5\n",
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/hands/Sess01/bold\n",
      "cmdline mri_binarize.bin --i masks/brain.nii.gz --o masks/brain.nii.gz --min 0.5 \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      masks/brain.nii.gz\n",
      "frame      0\n",
      "nErode3d   0\n",
      "nErode2d   0\n",
      "output     masks/brain.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        0.5\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n",
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 99815 values in range\n",
      "Counting number of voxels in first frame\n",
      "Found 99815 voxels in final mask\n",
      "Count: 99815 798520.000000 655360 15.230560\n",
      "mri_binarize done\n",
      "Diliating 1\n",
      "mri_binarize --i masks/brain.nii.gz --min 0.5 --dilate 1 --o masks/brain.nii.gz\n",
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/hands/Sess01/bold\n",
      "cmdline mri_binarize.bin --i masks/brain.nii.gz --min 0.5 --dilate 1 --o masks/brain.nii.gz \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      masks/brain.nii.gz\n",
      "frame      0\n",
      "nErode3d   0\n",
      "nErode2d   0\n",
      "output     masks/brain.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        0.5\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n",
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 99815 values in range\n",
      "Dilating 1 voxels in 3d\n",
      "Counting number of voxels in first frame\n",
      "Found 127517 voxels in final mask\n",
      "Count: 127517 1020136.000000 655360 19.457550\n",
      "mri_binarize done\n",
      " \n",
      "Started at Fri Nov 24 13:08:11 CET 2017 \n",
      "Ended   at Fri Nov 24 13:08:12 CET 2017\n",
      "Mkbrainmask-Run-Time-Sec 1\n",
      " \n",
      "mkbrainmask Done\n",
      "mri_binarize --i masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o masks/brain.e3.nii.gz\n",
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/hands/Sess01/bold\n",
      "cmdline mri_binarize.bin --i masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o masks/brain.e3.nii.gz \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      masks/brain.nii.gz\n",
      "frame      0\n",
      "nErode3d   3\n",
      "nErode2d   0\n",
      "output     masks/brain.e3.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        0.5\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n",
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 123541 values in range\n",
      "Eroding 3 voxels in 3d\n",
      "Counting number of voxels in first frame\n",
      "Found 68587 voxels in final mask\n",
      "Count: 68587 548696.000000 655360 10.465546\n",
      "mri_binarize done\n",
      "mkbrainmask -i 005/template.nii.gz -o 005/masks/brain.nii.gz -reg /data/martin/prosopagnosia/hands/Sess01/bold/005/register.dof6.lta -ndil 1 -nerode 0\n",
      "Fri Nov 24 13:08:12 CET 2017\n",
      "\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/hands/Sess01/bold\n",
      "/usr/local/freesurfer/fsfast/bin/mkbrainmask -i 005/template.nii.gz -o 005/masks/brain.nii.gz -reg /data/martin/prosopagnosia/hands/Sess01/bold/005/register.dof6.lta -ndil 1 -nerode 0\n",
      "\n",
      "freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c\n",
      "$Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "mri_vol2vol --mov 005/template.nii.gz --reg /data/martin/prosopagnosia/hands/Sess01/bold/005/register.dof6.lta --inv --interp nearest --o 005/masks/brain.nii.gz --targ /usr/local/freesurfer/subjects/pBrain/mri/aparc+aseg.mgz\n",
      "regio_read_register: loading lta\n",
      "\n",
      "Matrix from regfile:\n",
      " 0.99931   0.03690  -0.00422   1.43463;\n",
      " 0.01380  -0.26354   0.96455  -20.42809;\n",
      "-0.03448   0.96394   0.26387   5.44201;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "movvol 005/template.nii.gz\n",
      "targvol /usr/local/freesurfer/subjects/pBrain/mri/aparc+aseg.mgz\n",
      "outvol 005/masks/brain.nii.gz\n",
      "regfile /data/martin/prosopagnosia/hands/Sess01/bold/005/register.dof6.lta\n",
      "invert 1\n",
      "tal    0\n",
      "talres 2\n",
      "regheader 0\n",
      "noresample 0\n",
      "interp  nearest (0)\n",
      "precision  float (3)\n",
      "Gdiag_no  -1\n",
      "Synth      0\n",
      "SynthSeed  1512058950\n",
      "\n",
      "Invert!\n",
      "Inverting registration\n",
      "\n",
      "Final tkRAS-to-tkRAS Matrix is:\n",
      " 0.99931   0.01380  -0.03448  -0.96399;\n",
      " 0.03690  -0.26354   0.96394  -10.68238;\n",
      "-0.00422   0.96455   0.26387   18.27396;\n",
      "-0.00000  -0.00000  -0.00000   1.00000;\n",
      "\n",
      "\n",
      "Vox2Vox Matrix is:\n",
      " 1.99862  -0.06897  -0.02761   6.01843;\n",
      "-0.00844   0.52774  -1.92910   115.07260;\n",
      "-0.07381  -1.92788  -0.52708   255.96759;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "\n",
      "Resampling\n",
      "Output registration matrix is identity\n",
      "\n",
      "mri_vol2vol done\n",
      "mri_binarize --i 005/masks/brain.nii.gz --o 005/masks/brain.nii.gz --min 0.5\n",
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/hands/Sess01/bold\n",
      "cmdline mri_binarize.bin --i 005/masks/brain.nii.gz --o 005/masks/brain.nii.gz --min 0.5 \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      005/masks/brain.nii.gz\n",
      "frame      0\n",
      "nErode3d   0\n",
      "nErode2d   0\n",
      "output     005/masks/brain.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        0.5\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n",
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 99735 values in range\n",
      "Counting number of voxels in first frame\n",
      "Found 99735 voxels in final mask\n",
      "Count: 99735 797880.000000 655360 15.218353\n",
      "mri_binarize done\n",
      "Diliating 1\n",
      "mri_binarize --i 005/masks/brain.nii.gz --min 0.5 --dilate 1 --o 005/masks/brain.nii.gz\n",
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/hands/Sess01/bold\n",
      "cmdline mri_binarize.bin --i 005/masks/brain.nii.gz --min 0.5 --dilate 1 --o 005/masks/brain.nii.gz \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      005/masks/brain.nii.gz\n",
      "frame      0\n",
      "nErode3d   0\n",
      "nErode2d   0\n",
      "output     005/masks/brain.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        0.5\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n",
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 99735 values in range\n",
      "Dilating 1 voxels in 3d\n",
      "Counting number of voxels in first frame\n",
      "Found 127356 voxels in final mask\n",
      "Count: 127356 1018848.000000 655360 19.432983\n",
      "mri_binarize done\n",
      " \n",
      "Started at Fri Nov 24 13:08:12 CET 2017 \n",
      "Ended   at Fri Nov 24 13:08:13 CET 2017\n",
      "Mkbrainmask-Run-Time-Sec 1\n",
      " \n",
      "mkbrainmask Done\n",
      "mri_binarize --i 005/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 005/masks/brain.e3.nii.gz\n",
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/hands/Sess01/bold\n",
      "cmdline mri_binarize.bin --i 005/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 005/masks/brain.e3.nii.gz \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      005/masks/brain.nii.gz\n",
      "frame      0\n",
      "nErode3d   3\n",
      "nErode2d   0\n",
      "output     005/masks/brain.e3.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        0.5\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n",
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 123392 values in range\n",
      "Eroding 3 voxels in 3d\n",
      "Counting number of voxels in first frame\n",
      "Found 68561 voxels in final mask\n",
      "Count: 68561 548488.000000 655360 10.461578\n",
      "mri_binarize done\n",
      "meanval --i 005/f.nii --m 005/masks/brain.e3.nii.gz --o 005/global.meanval.dat --avgwf 005/global.waveform.dat\n",
      "Fri Nov 24 13:08:13 CET 2017\n",
      "\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/hands/Sess01/bold\n",
      "/usr/local/freesurfer/bin/meanval --i 005/f.nii --m 005/masks/brain.e3.nii.gz --o 005/global.meanval.dat --avgwf 005/global.waveform.dat\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "mri_segstats --seg 005/masks/brain.e3.nii.gz --id 1 --sum /data/martin/prosopagnosia/hands/Sess01/bold/005/tmpdir.meanval.28001/blah.28001 --in 005/f.nii --sfavg 005/global.meanval.dat --avgwf 005/global.waveform.dat\n",
      "\n",
      "$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $\n",
      "cwd \n",
      "cmdline mri_segstats --seg 005/masks/brain.e3.nii.gz --id 1 --sum /data/martin/prosopagnosia/hands/Sess01/bold/005/tmpdir.meanval.28001/blah.28001 --in 005/f.nii --sfavg 005/global.meanval.dat --avgwf 005/global.waveform.dat \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "UseRobust  0\n",
      "Loading 005/masks/brain.e3.nii.gz\n",
      "Loading 005/f.nii\n",
      "Voxel Volume is 8 mm^3\n",
      "Generating list of segmentation ids\n",
      "Found   1 segmentations\n",
      "Computing statistics for each segmentation\n",
      "\n",
      "Reporting on   1 segmentations\n",
      "Using PrintSegStat\n",
      "Computing spatial average of each frame\n",
      "  0\n",
      "Writing to 005/global.meanval.dat\n",
      "0 824.69\n",
      "Writing to 005/global.waveform.dat\n",
      "mri_segstats done\n",
      "Fri Nov 24 13:08:21 CET 2017\n",
      "mkbrainmask-sess done\n",
      "Sess01 MC -----------------------------\n",
      "mc-sess -fstem f -fmcstem fmcpr -s Sess01 -d /data/martin/prosopagnosia/hands -fsd bold -per-run -update\n",
      "Logfile is /data/martin/prosopagnosia/hands/log/mc-Sess01-bold.log\n",
      "-------------------------------------------\n",
      "/data/martin/prosopagnosia/hands/Sess01 \n",
      "RunList: 005\n",
      "  ------- ************************** -----------\n",
      "  ------- Motion Correcting Run 005 -----------\n",
      "  ------- ************************** -----------\n",
      "sess = Sess01\n",
      "Fri Nov 24 13:08:21 CET 2017\n",
      "mc-afni2 --i 005/f.nii --t 005/template.nii.gz --o 005/fmcpr.nii.gz --mcdat 005/fmcpr.mcdat\n",
      "/data/martin/prosopagnosia/hands/Sess01/bold\n",
      "mri_info --nframes --o /tmp/mriinfo.28101 005/template.nii.gz\n",
      "log file is 005/fmcpr.nii.gz.mclog\n",
      "mcdat file is 005/fmcpr.mcdat\n",
      "tmp dir is 005/tmp.mc-afni2.28101\n",
      "#@# --------------------------------\n",
      "/data/martin/prosopagnosia/hands/Sess01/bold\n",
      "mri_convert 005/template.nii.gz 005/tmp.mc-afni2.28101/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float\n",
      "mri_convert.bin 005/template.nii.gz 005/tmp.mc-afni2.28101/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float \n",
      "nskip = 0\n",
      "ndrop = 0\n",
      "$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $\n",
      "reading from 005/template.nii.gz...\n",
      "TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00\n",
      "i_ras = (-0.999463, -0.0273032, 0.0181267)\n",
      "j_ras = (0.022681, -0.975511, -0.21878)\n",
      "k_ras = (0.0236561, -0.218251, 0.975606)\n",
      "changing data type from short to float (noscale = 0)...\n",
      "writing to 005/tmp.mc-afni2.28101/tempvol.nii.gz...\n",
      "#@# --------------------------------\n",
      "/data/martin/prosopagnosia/hands/Sess01/bold\n",
      "mri_convert 005/f.nii 005/tmp.mc-afni2.28101/invol.nii.gz -odt float\n",
      "mri_convert.bin 005/f.nii 005/tmp.mc-afni2.28101/invol.nii.gz -odt float \n",
      "$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $\n",
      "reading from 005/f.nii...\n",
      "TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00\n",
      "i_ras = (-0.999463, -0.0273032, 0.0181267)\n",
      "j_ras = (0.022681, -0.975511, -0.21878)\n",
      "k_ras = (0.0236561, -0.218251, 0.975606)\n",
      "changing data type from short to float (noscale = 0)...\n",
      "writing to 005/tmp.mc-afni2.28101/invol.nii.gz...\n",
      "#@# --------------------------------\n",
      "/data/martin/prosopagnosia/hands/Sess01/bold\n",
      "3dvolreg.afni -verbose -dfile 005/fmcpr.mcdat -1Dmatrix_save 005/fmcpr.mat -base 005/tmp.mc-afni2.28101/tempvol.nii.gz -prefix 005/tmp.mc-afni2.28101/outvol.nii.gz 005/tmp.mc-afni2.28101/invol.nii.gz\n",
      "++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Aug 29 2012) [64-bit]\n",
      "++ Authored by: RW Cox\n",
      "*+ WARNING:   If you are performing spatial transformations on an oblique dset, \n",
      "  such as 005/tmp.mc-afni2.28101/tempvol.nii.gz,\n",
      "  or viewing/combining it with volumes of differing obliquity,\n",
      "  you should consider running: \n",
      "     3dWarp -deoblique \n",
      "  on this and  other oblique datasets in the same session.\n",
      " See 3dWarp -help for details.\n",
      "++ Oblique dataset:005/tmp.mc-afni2.28101/tempvol.nii.gz is 12.706240 degrees from plumb.\n",
      "++ Reading in base dataset 005/tmp.mc-afni2.28101/tempvol.nii.gz\n",
      "++ Oblique dataset:005/tmp.mc-afni2.28101/invol.nii.gz is 12.706240 degrees from plumb.\n",
      "++ Reading input dataset 005/tmp.mc-afni2.28101/invol.nii.gz\n",
      "++ Edging: x=6 y=6 z=2\n",
      "++ Creating mask for -maxdisp\n",
      " + Automask has 123973 voxels\n",
      " + 14090 voxels left in -maxdisp mask after erosion\n",
      "++ Initializing alignment base\n",
      "++ Starting final pass on 197 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..\n",
      "++ CPU time for realignment=0 s  [=0 s/sub-brick]\n",
      "++ Min : roll=-0.049  pitch=-0.116  yaw=-0.050  dS=-0.043  dL=-0.049  dP=-0.208\n",
      "++ Mean: roll=+0.021  pitch=+0.011  yaw=+0.053  dS=+0.124  dL=-0.004  dP=-0.023\n",
      "++ Max : roll=+0.127  pitch=+0.142  yaw=+0.130  dS=+0.295  dL=+0.043  dP=+0.162\n",
      "++ Max displacements (mm) for each sub-brick:\n",
      " 0.26 0.28 0.24 0.29 0.23 0.29 0.21 0.25 0.28 0.28 0.25 0.24 0.26 0.27 0.35 0.37 0.23 0.22 0.24 0.32 0.27 0.32 0.33 0.31 0.31 0.30 0.28 0.29 0.29 0.26 0.23 0.25 0.27 0.26 0.30 0.31 0.26 0.25 0.34 0.35 0.29 0.33 0.14 0.15 0.16 0.20 0.23 0.20 0.16 0.15 0.11 0.14 0.18 0.18 0.12 0.17 0.17 0.17 0.18 0.16 0.21 0.22 0.28 0.25 0.30 0.32 0.29 0.27 0.30 0.27 0.27 0.26 0.24 0.22 0.25 0.25 0.31 0.27 0.25 0.26 0.23 0.15 0.17 0.21 0.18 0.20 0.19 0.16 0.13 0.16 0.15 0.14 0.16 0.16 0.12 0.18 0.09 0.03 0.00 0.07 0.20 0.15 0.16 0.22 0.23 0.24 0.26 0.28 0.28 0.38 0.32 0.27 0.27 0.29 0.26 0.26 0.25 0.23 0.22 0.24 0.26 0.24 0.25 0.22 0.23 0.23 0.26 0.24 0.25 0.28 0.28 0.27 0.25 0.26 0.27 0.26 0.28 0.27 0.28 0.28 0.28 0.28 0.29 0.28 0.28 0.28 0.27 0.26 0.26 0.27 0.29 0.27 0.29 0.30 0.35 0.34 0.31 0.35 0.31 0.25 0.27 0.30 0.31 0.32 0.31 0.35 0.26 0.21 0.20 0.17 0.17 0.17 0.16 0.15 0.23 0.24 0.32 0.27 0.22 0.26 0.26 0.19 0.25 0.29 0.34 0.40 0.34 0.35 0.17 0.24 0.17 0.20 0.35 0.20 0.29 0.25 0.30\n",
      "++ Max displacement in automask = 0.40 (mm) at sub-brick 185\n",
      "++ Wrote dataset to disk in 005/tmp.mc-afni2.28101/outvol.nii.gz\n",
      "#@# --------------------------------\n",
      "/data/martin/prosopagnosia/hands/Sess01/bold\n",
      "mri_convert 005/tmp.mc-afni2.28101/outvol.nii.gz 005/fmcpr.nii.gz --in_like 005/template.nii.gz\n",
      "mri_convert.bin 005/tmp.mc-afni2.28101/outvol.nii.gz 005/fmcpr.nii.gz --in_like 005/template.nii.gz \n",
      "reading info from 005/template.nii.gz...\n",
      "$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $\n",
      "reading from 005/tmp.mc-afni2.28101/outvol.nii.gz...\n",
      "TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00\n",
      "INFO: frames are not the same\n",
      "i_ras = (-0.999463, -0.0273032, 0.0181267)\n",
      "j_ras = (0.022681, -0.975511, -0.21878)\n",
      "k_ras = (0.0236561, -0.218251, 0.975606)\n",
      "writing to 005/fmcpr.nii.gz...\n",
      "... cleaning up ....\n",
      "Fri Nov 24 13:10:26 CET 2017\n",
      "mc-afni2 done\n",
      "INFO: Making external regressor from mc params\n",
      "mcdat2mcextreg --i 005/fmcpr.mcdat --o 005/mcprextreg\n",
      "Fri Nov 24 13:10:26 CET 2017\n",
      "\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/hands/Sess01/bold\n",
      "/usr/local/freesurfer/fsfast/bin/mcdat2mcextreg --i 005/fmcpr.mcdat --o 005/mcprextreg\n",
      "\n",
      "freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "mri_glmfit --table /data/martin/prosopagnosia/hands/Sess01/bold/005/tmpdir.mcdat2extreg.28443/table.dat --glmdir /data/martin/prosopagnosia/hands/Sess01/bold/005/tmpdir.mcdat2extreg.28443/glm --osgm --y-out /data/martin/prosopagnosia/hands/Sess01/bold/005/tmpdir.mcdat2extreg.28443/y.out.nii --pca\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $\n",
      "cwd /data/martin/prosopagnosia/hands/Sess01/bold\n",
      "cmdline mri_glmfit.bin --table /data/martin/prosopagnosia/hands/Sess01/bold/005/tmpdir.mcdat2extreg.28443/table.dat --glmdir /data/martin/prosopagnosia/hands/Sess01/bold/005/tmpdir.mcdat2extreg.28443/glm --osgm --y-out /data/martin/prosopagnosia/hands/Sess01/bold/005/tmpdir.mcdat2extreg.28443/y.out.nii --pca \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "FixVertexAreaFlag = 1\n",
      "UseMaskWithSmoothing     1\n",
      "OneSampleGroupMean 1\n",
      "y    /data/martin/prosopagnosia/hands/Sess01/bold/005/tmpdir.mcdat2extreg.28443/table.dat\n",
      "logyflag 0\n",
      "usedti  0\n",
      "glmdir /data/martin/prosopagnosia/hands/Sess01/bold/005/tmpdir.mcdat2extreg.28443/glm\n",
      "IllCondOK 0\n",
      "ReScaleX 1\n",
      "DoFFx 0\n",
      "Creating output directory /data/martin/prosopagnosia/hands/Sess01/bold/005/tmpdir.mcdat2extreg.28443/glm\n",
      "Loading y from /data/martin/prosopagnosia/hands/Sess01/bold/005/tmpdir.mcdat2extreg.28443/table.dat\n",
      "Found 6 data colums\n",
      "Found 197 data rows\n",
      "Saving design matrix to /data/martin/prosopagnosia/hands/Sess01/bold/005/tmpdir.mcdat2extreg.28443/glm/Xg.dat\n",
      "Computing normalized matrix\n",
      "Normalized matrix condition is 1\n",
      "Matrix condition is 1\n",
      "search space = 6.000000\n",
      "DOF = 196\n",
      "Starting fit and test\n",
      "Fit completed in 0 minutes\n",
      "Writing results\n",
      "  osgm\n",
      "    maxvox sig=1e+10  F=1108.31  at  index 3 0 0    seed=1511591292\n",
      "Measure:MC                        osgm \n",
      "Tx                                 11.618 \n",
      "Ty                                  2.485 \n",
      "Tz                                 44.154 \n",
      "Rx                                10000000000.000 \n",
      "Ry                                 -3.417 \n",
      "Rz                                 -7.065 \n",
      "Computing PCA (197)\n",
      "mri_glmfit done\n",
      "ninputs = 1\n",
      "Checking inputs\n",
      "nframestot = 197\n",
      "Allocing output\n",
      "Done allocing\n",
      "nframes = 197\n",
      "Computing PCA\n",
      "Writing to /data/martin/prosopagnosia/hands/Sess01/bold/005/tmpdir.mcdat2extreg.28443/pca.nii\n",
      "mcdat2mcextreg done\n",
      "\n",
      "\n",
      "Fri Nov 24 13:10:26 CET 2017\n",
      "mc-sess completed SUCCESSFULLY\n",
      "Sess01 To Surface -----------------------------\n",
      "rawfunc2surf-sess -fwhm 5 -s Sess01 -d /data/martin/prosopagnosia/hands -fsd bold -trgsubject pBrain -update -per-run\n",
      "instem fmcpr\n",
      "outstem fmcpr.sm5.pBrain.hemi\n",
      "------------------------------ \n",
      "1/1 Sess01\n",
      "  1/1 Sess01 005 lh ---------\n",
      "    Fri Nov 24 13:10:26 CET 2017\n",
      "mri_vol2surf --mov /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.nii.gz --reg /data/martin/prosopagnosia/hands/Sess01/bold/005/register.dof6.lta --trgsubject pBrain --interp nearest --projfrac 0.5 --hemi lh --o /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.lh.pr.nii.gz --noreshape --cortex\n",
      "srcvol = /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.nii.gz\n",
      "srcreg = /data/martin/prosopagnosia/hands/Sess01/bold/005/register.dof6.lta\n",
      "srcregold = 0\n",
      "srcwarp unspecified\n",
      "surf = white\n",
      "hemi = lh\n",
      "trgsubject = pBrain\n",
      "surfreg = sphere.reg\n",
      "ProjFrac = 0.5\n",
      "thickness = thickness\n",
      "reshape = 0\n",
      "interp = nearest\n",
      "float2int = round\n",
      "GetProjMax = 0\n",
      "INFO: float2int code = 0\n",
      "INFO: changing type to float\n",
      "Done loading volume\n",
      "Input reg is LTA\n",
      "-------- original matrix -----------\n",
      " 0.99931   0.03690  -0.00422   1.43463;\n",
      " 0.01380  -0.26354   0.96455  -20.42809;\n",
      "-0.03448   0.96394   0.26387   5.44202;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "-------- original matrix -----------\n",
      "Loading label /usr/local/freesurfer/subjects/pBrain/label/lh.cortex.label\n",
      "Reading surface /usr/local/freesurfer/subjects/pBrain/surf/lh.white\n",
      "Done reading source surface\n",
      "Reading thickness /usr/local/freesurfer/subjects/pBrain/surf/lh.thickness\n",
      "Done\n",
      "Mapping Source Volume onto Source Subject Surface\n",
      " 1 0.5 0.5 0.5\n",
      "using old\n",
      "Done mapping volume to surface\n",
      "Number of source voxels hit = 19336\n",
      "Masking with /usr/local/freesurfer/subjects/pBrain/label/lh.cortex.label\n",
      "Writing to /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.lh.pr.nii.gz\n",
      "Dim: 112635 1 1\n",
      "mri_binarize --i /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.lh.pr.nii.gz --min .00001 --o /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.lh.pr.nii.gz\n",
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/hands\n",
      "cmdline mri_binarize.bin --i /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.lh.pr.nii.gz --min .00001 --o /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.lh.pr.nii.gz \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.lh.pr.nii.gz\n",
      "frame      0\n",
      "nErode3d   0\n",
      "nErode2d   0\n",
      "output     /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.lh.pr.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        1e-05\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n",
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 82533 values in range\n",
      "Counting number of voxels in first frame\n",
      "Found 82533 voxels in final mask\n",
      "Count: 82533 82533.000000 112635 73.274737\n",
      "mri_binarize done\n",
      "mri_concat --o /data/martin/prosopagnosia/hands/Sess01/bold/masks/brain.pBrain.lh.pr.nii.gz --mean /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.lh.pr.nii.gz\n",
      "ninputs = 1\n",
      "Checking inputs\n",
      "nframestot = 1\n",
      "Allocing output\n",
      "Done allocing\n",
      "nframes = 1\n",
      "Computing mean across frames\n",
      "Writing to /data/martin/prosopagnosia/hands/Sess01/bold/masks/brain.pBrain.lh.pr.nii.gz\n",
      "mri_binarize --i /data/martin/prosopagnosia/hands/Sess01/bold/masks/brain.pBrain.lh.pr.nii.gz --min 10e-10 --o /data/martin/prosopagnosia/hands/Sess01/bold/masks/brain.pBrain.lh.pr.nii.gz\n",
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/hands\n",
      "cmdline mri_binarize.bin --i /data/martin/prosopagnosia/hands/Sess01/bold/masks/brain.pBrain.lh.pr.nii.gz --min 10e-10 --o /data/martin/prosopagnosia/hands/Sess01/bold/masks/brain.pBrain.lh.pr.nii.gz \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      /data/martin/prosopagnosia/hands/Sess01/bold/masks/brain.pBrain.lh.pr.nii.gz\n",
      "frame      0\n",
      "nErode3d   0\n",
      "nErode2d   0\n",
      "output     /data/martin/prosopagnosia/hands/Sess01/bold/masks/brain.pBrain.lh.pr.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        1e-09\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n",
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 82533 values in range\n",
      "Counting number of voxels in first frame\n",
      "Found 82533 voxels in final mask\n",
      "Count: 82533 82533.000000 112635 73.274737\n",
      "mri_binarize done\n",
      "  1/1 Sess01 005 rh ---------\n",
      "    Fri Nov 24 13:10:27 CET 2017\n",
      "mri_vol2surf --mov /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.nii.gz --reg /data/martin/prosopagnosia/hands/Sess01/bold/005/register.dof6.lta --trgsubject pBrain --interp nearest --projfrac 0.5 --hemi rh --o /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.rh.pr.nii.gz --noreshape --cortex\n",
      "srcvol = /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.nii.gz\n",
      "srcreg = /data/martin/prosopagnosia/hands/Sess01/bold/005/register.dof6.lta\n",
      "srcregold = 0\n",
      "srcwarp unspecified\n",
      "surf = white\n",
      "hemi = rh\n",
      "trgsubject = pBrain\n",
      "surfreg = sphere.reg\n",
      "ProjFrac = 0.5\n",
      "thickness = thickness\n",
      "reshape = 0\n",
      "interp = nearest\n",
      "float2int = round\n",
      "GetProjMax = 0\n",
      "INFO: float2int code = 0\n",
      "INFO: changing type to float\n",
      "Done loading volume\n",
      "Input reg is LTA\n",
      "-------- original matrix -----------\n",
      " 0.99931   0.03690  -0.00422   1.43463;\n",
      " 0.01380  -0.26354   0.96455  -20.42809;\n",
      "-0.03448   0.96394   0.26387   5.44202;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "-------- original matrix -----------\n",
      "Loading label /usr/local/freesurfer/subjects/pBrain/label/rh.cortex.label\n",
      "Reading surface /usr/local/freesurfer/subjects/pBrain/surf/rh.white\n",
      "Done reading source surface\n",
      "Reading thickness /usr/local/freesurfer/subjects/pBrain/surf/rh.thickness\n",
      "Done\n",
      "Mapping Source Volume onto Source Subject Surface\n",
      " 1 0.5 0.5 0.5\n",
      "using old\n",
      "Done mapping volume to surface\n",
      "Number of source voxels hit = 19063\n",
      "Masking with /usr/local/freesurfer/subjects/pBrain/label/rh.cortex.label\n",
      "Writing to /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.rh.pr.nii.gz\n",
      "Dim: 111586 1 1\n",
      "mri_binarize --i /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.rh.pr.nii.gz --min .00001 --o /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.rh.pr.nii.gz\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/hands\n",
      "cmdline mri_binarize.bin --i /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.rh.pr.nii.gz --min .00001 --o /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.rh.pr.nii.gz \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.rh.pr.nii.gz\n",
      "frame      0\n",
      "nErode3d   0\n",
      "nErode2d   0\n",
      "output     /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.rh.pr.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        1e-05\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n",
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 81954 values in range\n",
      "Counting number of voxels in first frame\n",
      "Found 81954 voxels in final mask\n",
      "Count: 81954 81954.000000 111586 73.444697\n",
      "mri_binarize done\n",
      "mri_concat --o /data/martin/prosopagnosia/hands/Sess01/bold/masks/brain.pBrain.rh.pr.nii.gz --mean /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.rh.pr.nii.gz\n",
      "ninputs = 1\n",
      "Checking inputs\n",
      "nframestot = 1\n",
      "Allocing output\n",
      "Done allocing\n",
      "nframes = 1\n",
      "Computing mean across frames\n",
      "Writing to /data/martin/prosopagnosia/hands/Sess01/bold/masks/brain.pBrain.rh.pr.nii.gz\n",
      "mri_binarize --i /data/martin/prosopagnosia/hands/Sess01/bold/masks/brain.pBrain.rh.pr.nii.gz --min 10e-10 --o /data/martin/prosopagnosia/hands/Sess01/bold/masks/brain.pBrain.rh.pr.nii.gz\n",
      "\n",
      "$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $\n",
      "cwd /data/martin/prosopagnosia/hands\n",
      "cmdline mri_binarize.bin --i /data/martin/prosopagnosia/hands/Sess01/bold/masks/brain.pBrain.rh.pr.nii.gz --min 10e-10 --o /data/martin/prosopagnosia/hands/Sess01/bold/masks/brain.pBrain.rh.pr.nii.gz \n",
      "sysname  Linux\n",
      "hostname dhcp-129-70-100-154\n",
      "machine  x86_64\n",
      "user     martin\n",
      "\n",
      "input      /data/martin/prosopagnosia/hands/Sess01/bold/masks/brain.pBrain.rh.pr.nii.gz\n",
      "frame      0\n",
      "nErode3d   0\n",
      "nErode2d   0\n",
      "output     /data/martin/prosopagnosia/hands/Sess01/bold/masks/brain.pBrain.rh.pr.nii.gz\n",
      "Binarizing based on threshold\n",
      "min        1e-09\n",
      "max        +infinity\n",
      "binval        1\n",
      "binvalnot     0\n",
      "fstart = 0, fend = 0, nframes = 1\n",
      "Found 81954 values in range\n",
      "Counting number of voxels in first frame\n",
      "Found 81954 voxels in final mask\n",
      "Count: 81954 81954.000000 111586 73.444697\n",
      "mri_binarize done\n",
      "  1/1 Sess01 005 lh ---------\n",
      "    Fri Nov 24 13:10:28 CET 2017\n",
      "mri_vol2surf --mov /data/martin/prosopagnosia/hands/Sess01/bold/005/fmcpr.nii.gz --reg /data/martin/prosopagnosia/hands/Sess01/bold/005/register.dof6.lta --trgsubject pBrain --interp trilin --projfrac 0.5 --hemi lh --o /data/martin/prosopagnosia/hands/Sess01/bold/005/fmcpr.sm5.pBrain.lh.nii.gz --noreshape --cortex\n",
      "srcvol = /data/martin/prosopagnosia/hands/Sess01/bold/005/fmcpr.nii.gz\n",
      "srcreg = /data/martin/prosopagnosia/hands/Sess01/bold/005/register.dof6.lta\n",
      "srcregold = 0\n",
      "srcwarp unspecified\n",
      "surf = white\n",
      "hemi = lh\n",
      "trgsubject = pBrain\n",
      "surfreg = sphere.reg\n",
      "ProjFrac = 0.5\n",
      "thickness = thickness\n",
      "reshape = 0\n",
      "interp = trilin\n",
      "float2int = round\n",
      "GetProjMax = 0\n",
      "INFO: float2int code = 0\n",
      "Done loading volume\n",
      "Input reg is LTA\n",
      "-------- original matrix -----------\n",
      " 0.99931   0.03690  -0.00422   1.43463;\n",
      " 0.01380  -0.26354   0.96455  -20.42809;\n",
      "-0.03448   0.96394   0.26387   5.44202;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "-------- original matrix -----------\n",
      "Loading label /usr/local/freesurfer/subjects/pBrain/label/lh.cortex.label\n",
      "Reading surface /usr/local/freesurfer/subjects/pBrain/surf/lh.white\n",
      "Done reading source surface\n",
      "Reading thickness /usr/local/freesurfer/subjects/pBrain/surf/lh.thickness\n",
      "Done\n",
      "Mapping Source Volume onto Source Subject Surface\n",
      " 1 0.5 0.5 0.5\n",
      "using old\n",
      "Done mapping volume to surface\n",
      "Number of source voxels hit = 19336\n",
      "Masking with /usr/local/freesurfer/subjects/pBrain/label/lh.cortex.label\n",
      "Writing to /data/martin/prosopagnosia/hands/Sess01/bold/005/fmcpr.sm5.pBrain.lh.nii.gz\n",
      "Dim: 112635 1 1\n",
      "mris_fwhm --s pBrain --hemi lh --smooth-only --i /data/martin/prosopagnosia/hands/Sess01/bold/005/fmcpr.sm5.pBrain.lh.nii.gz --fwhm 5 --o /data/martin/prosopagnosia/hands/Sess01/bold/005/fmcpr.sm5.pBrain.lh.nii.gz --mask /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.lh.nii.gz --no-detrend\n",
      "pBrain lh white\n",
      "Number of vertices 112635\n",
      "Number of faces    225266\n",
      "Total area         74093.468750\n",
      "GroupSurface 0\n",
      "AvgVtxArea       0.657819\n",
      "AvgVtxDist       0.887337\n",
      "StdVtxDist       0.259981\n",
      "Loading mask /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.lh.nii.gz\n",
      "Found 82533 voxels in mask\n",
      "Not Polynomial detrending\n",
      "Smoothing input by fwhm=5.000000, gstd=2.123305, niters=14 \n",
      "Only smoothing, so saving and exiting now\n",
      "  1/1 Sess01 005 rh ---------\n",
      "    Fri Nov 24 13:10:46 CET 2017\n",
      "mri_vol2surf --mov /data/martin/prosopagnosia/hands/Sess01/bold/005/fmcpr.nii.gz --reg /data/martin/prosopagnosia/hands/Sess01/bold/005/register.dof6.lta --trgsubject pBrain --interp trilin --projfrac 0.5 --hemi rh --o /data/martin/prosopagnosia/hands/Sess01/bold/005/fmcpr.sm5.pBrain.rh.nii.gz --noreshape --cortex\n",
      "srcvol = /data/martin/prosopagnosia/hands/Sess01/bold/005/fmcpr.nii.gz\n",
      "srcreg = /data/martin/prosopagnosia/hands/Sess01/bold/005/register.dof6.lta\n",
      "srcregold = 0\n",
      "srcwarp unspecified\n",
      "surf = white\n",
      "hemi = rh\n",
      "trgsubject = pBrain\n",
      "surfreg = sphere.reg\n",
      "ProjFrac = 0.5\n",
      "thickness = thickness\n",
      "reshape = 0\n",
      "interp = trilin\n",
      "float2int = round\n",
      "GetProjMax = 0\n",
      "INFO: float2int code = 0\n",
      "Done loading volume\n",
      "Input reg is LTA\n",
      "-------- original matrix -----------\n",
      " 0.99931   0.03690  -0.00422   1.43463;\n",
      " 0.01380  -0.26354   0.96455  -20.42809;\n",
      "-0.03448   0.96394   0.26387   5.44202;\n",
      " 0.00000   0.00000   0.00000   1.00000;\n",
      "-------- original matrix -----------\n",
      "Loading label /usr/local/freesurfer/subjects/pBrain/label/rh.cortex.label\n",
      "Reading surface /usr/local/freesurfer/subjects/pBrain/surf/rh.white\n",
      "Done reading source surface\n",
      "Reading thickness /usr/local/freesurfer/subjects/pBrain/surf/rh.thickness\n",
      "Done\n",
      "Mapping Source Volume onto Source Subject Surface\n",
      " 1 0.5 0.5 0.5\n",
      "using old\n",
      "Done mapping volume to surface\n",
      "Number of source voxels hit = 19063\n",
      "Masking with /usr/local/freesurfer/subjects/pBrain/label/rh.cortex.label\n",
      "Writing to /data/martin/prosopagnosia/hands/Sess01/bold/005/fmcpr.sm5.pBrain.rh.nii.gz\n",
      "Dim: 111586 1 1\n",
      "mris_fwhm --s pBrain --hemi rh --smooth-only --i /data/martin/prosopagnosia/hands/Sess01/bold/005/fmcpr.sm5.pBrain.rh.nii.gz --fwhm 5 --o /data/martin/prosopagnosia/hands/Sess01/bold/005/fmcpr.sm5.pBrain.rh.nii.gz --mask /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.rh.nii.gz --no-detrend\n",
      "pBrain rh white\n",
      "Number of vertices 111586\n",
      "Number of faces    223168\n",
      "Total area         73917.976562\n",
      "GroupSurface 0\n",
      "AvgVtxArea       0.662431\n",
      "AvgVtxDist       0.889571\n",
      "StdVtxDist       0.264496\n",
      "Loading mask /data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.rh.nii.gz\n",
      "Found 81954 voxels in mask\n",
      "Not Polynomial detrending\n",
      "Smoothing input by fwhm=5.000000, gstd=2.123305, niters=14 \n",
      "Only smoothing, so saving and exiting now\n",
      "\n",
      "Fri Nov 24 13:11:05 CET 2017\n",
      "rawfunc2surf-sess completed \n",
      "----------------------------------------\n",
      "Started at Fri Nov 24 13:05:35 CET 2017\n",
      "Ended   at Fri Nov 24 13:11:05 CET 2017\n",
      "preproc-sess done\n"
     ]
    }
   ],
   "source": [
    "preproc-sess -sf sessids -surface pBrain lhrh -fwhm 5 -per-run -fsd bold"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "analysis"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting TER to 0.050000\n",
      "Setting TimeWindow to 40.000000\n",
      "Setting PreStim    to 0\n",
      "Setting PostStim   to 40.000000\n",
      "# FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c\n",
      "# MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $\n",
      "# MKACMD /usr/local/freesurfer/fsfast/bin/mkanalysis-sess -analysis design.sm5.rh -surface pBrain rh -per-run -fwhm 5 -fsd bold -paradigm design.par -event-related -spmhrf 0 -refeventdur 12 -polyfit 2 -mcextreg -nskip 0 -TR 3 -nconditions 1\n",
      "# DATE Fri Nov 24 13:11:06 CET 2017\n",
      "\n",
      "analysis design.sm5.rh\n",
      "mcstem fmcpr\n",
      "fsd bold\n",
      "TR 3\n",
      "RegDOF 6\n",
      "PerSession 0\n",
      "RawSpace surface pBrain rh\n",
      "mask brain\n",
      "RawFWHM 5\n",
      "RawSTC none\n",
      "nSliceGroups 1\n",
      "UseB0DC 0\n",
      "ApplySubCortMask 1\n",
      "inorm 100\n",
      "acfbins 30\n",
      "fixacf  1\n",
      "acffwhm 20\n",
      "acfsvd  0\n",
      "designtype event-related\n",
      "nskip 0\n",
      "polyfit 2\n",
      "HPFCutoffHz 0\n",
      "HeteroGCor 0\n",
      "nconditions 1\n",
      "parname design.par\n",
      "RefEventDur 12\n",
      "timewindow 40.000000\n",
      "prestim 0\n",
      "TER 0.050000\n",
      "spmhrf 0\n",
      "stimulusdelay -1.50000000000000000000\n",
      "Condition 1 Condition01\n",
      "nuisreg mcprextreg 3\n",
      "mkanalysis-sess done\n",
      "INFO: Found 1 Non-Null Conditions\n",
      "INFO: Found 1 Delays\n",
      "Condition Weights: 1.00000000000000000000\n",
      "mkcontrast2 -config design.sm5.rh/act-vs-rest.config -anadir design.sm5.rh -wcond 1.00000000000000000000 -sumconds -o design.sm5.rh/act-vs-rest.mat -wdelay 1 -no-octave\n",
      "  $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $\n",
      "cmtxfile  design.sm5.rh/act-vs-rest.mat\n",
      "nconds    1,  wcond  1.00000000000000000000\n",
      "ndelays   1, wdelay 1\n",
      "ndelays   1, wpsa   \n",
      "sumconds  1\n",
      "sumdelays 0\n",
      "nircorr   0\n",
      "TER       0.050000\n",
      "rdelta    \n",
      "rtau      \n",
      "  cmtxfile  design.sm5.rh/act-vs-rest.mat\n",
      "  monly  0\n",
      "  NCond   1\n",
      "  WCond   1.00000000000000000000\n",
      "  NDelay  1\n",
      "  WDelay  1\n",
      "  TER         0.050000\n",
      "  sumconds   1\n",
      "  sumdelays  0\n",
      "  nircorr  0\n",
      "  TPreStim  0\n",
      "  RmPreStim  0\n",
      "  rdelta     0 0\n",
      "  rtau       0 0\n",
      "  ndelays    1\n",
      "  CNorm      1\n",
      "  setwdelay  0\n",
      "  setwcond   0\n",
      "Matlab file is /tmp/mkcontrast2.28959.m\n",
      "MATLAB is selecting SOFTWARE OPENGL rendering.\n",
      "\n",
      "                            < M A T L A B (R) >\n",
      "                  Copyright 1984-2016 The MathWorks, Inc.\n",
      "                   R2016a (9.0.0.341360) 64-bit (glnxa64)\n",
      "                             February 11, 2016\n",
      "\n",
      " \n",
      "To get started, type one of these: helpwin, helpdesk, or demo.\n",
      "For product information, visit www.mathworks.com.\n",
      " \n",
      "\n",
      "\tThis is a Classroom License for instructional use only.\n",
      "\tResearch and commercial use is prohibited.\n",
      "\n",
      ">> starting mkcontrast2m\n",
      "Normalizing contrast matrix\n",
      "mkcontrast2m done\n",
      ">> Fri Nov 24 13:11:14 CET 2017\n",
      "Surface data pBrain rh\n",
      "--------------------------------------------------------------\n",
      "selxavg3-sess logfile is /data/martin/prosopagnosia/hands/log/selxavg3-sess-bold-design.sm5.rh-171124131114.log\n",
      "--------------------------------------------------------------\n",
      "selxavg3-sess log file\n",
      "/usr/local/freesurfer/fsfast/bin/selxavg3-sess\n",
      "-sf sessids -analysis design.sm5.rh\n",
      "$Id: selxavg3-sess,v 1.68 2016/05/10 03:24:18 greve Exp $\n",
      "uid=1000(martin) gid=1000(martin) groups=1000(martin),24(cdrom),25(floppy),29(audio),30(dip),44(video),46(plugdev),108(netdev),110(lpadmin),113(scanner),117(bluetooth),999(docker)\n",
      "/data/martin/prosopagnosia/hands\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "Fri Nov 24 13:11:14 CET 2017\n",
      "preproc-sess -s Sess01 -d /data/martin/prosopagnosia/hands -a design.sm5.rh -nolog\n",
      "--------------------------------------------------------------\n",
      "preproc-sess logfile is /dev/null\n",
      "--------------------------------------------------------------\n",
      "$Id: preproc-sess,v 1.64.2.1 2016/08/02 21:19:09 greve Exp $\n",
      "martin\n",
      "setenv FREESURFER_HOME /usr/local/freesurfer\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "/data/martin/prosopagnosia/hands\n",
      "/usr/local/freesurfer/fsfast/bin/preproc-sess\n",
      "-s Sess01 -d /data/martin/prosopagnosia/hands -a design.sm5.rh -nolog\n",
      "Fri Nov 24 13:11:14 CET 2017\n",
      "instem   f \n",
      "mc   1     f fmcpr \n",
      "stc  0     fmcpr\n",
      "sm   0   \n",
      "mask 1   brain\n",
      "Sess01 Template -----------------------------\n",
      "mktemplate-sess -s Sess01 -d /data/martin/prosopagnosia/hands -fsd bold -nolog -update\n",
      " \n",
      "Session: /data/martin/prosopagnosia/hands/Sess01 ----------------\n",
      "Fri Nov 24 13:11:14 CET 2017\n",
      "Detected input format at nii\n",
      "Sess01 Update not needed\n",
      "  Run: 005 ----------------\n",
      "  Fri Nov 24 13:11:14 CET 2017\n",
      "  Sess01 005 Update not needed\n",
      "Fri Nov 24 13:11:14 CET 2017\n",
      "mktemplate-sess completed \n",
      "Sess01 Registration -----------------------------\n",
      "register-sess -s Sess01 -d /data/martin/prosopagnosia/hands -fsd bold -delete-dat -dof 6 -bold -per-run -nolog -update -init-coreg\n",
      "--------------------------------------------------------------\n",
      "register-sess logfile is /dev/null\n",
      "--------------------------------------------------------------\n",
      "Fri Nov 24 13:11:14 CET 2017\n",
      "\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/hands\n",
      "/usr/local/freesurfer/fsfast/bin/register-sess -s Sess01 -d /data/martin/prosopagnosia/hands -fsd bold -delete-dat -dof 6 -bold -per-run -nolog -update -init-coreg\n",
      "\n",
      "freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      " \n",
      "Session: /data/martin/prosopagnosia/hands/Sess01 ----------------\n",
      "Fri Nov 24 13:11:14 CET 2017\n",
      "/data/martin/prosopagnosia/hands/Sess01\n",
      "  Run: 005 ----------------\n",
      "Fri Nov 24 13:11:14 CET 2017\n",
      "Update not needed\n",
      "Fri Nov 24 13:11:14 CET 2017\n",
      "register-sess completed \n",
      "Sess01 Mask ------------------------\n",
      "mkbrainmask-sess -maskstem brain -fsd bold -s Sess01 -d /data/martin/prosopagnosia/hands -per-run -nolog -update\n",
      "------------------------------------------------\n",
      "/data/martin/prosopagnosia/hands/Sess01 \n",
      "Fri Nov 24 13:11:14 CET 2017\n",
      "Sess01 Update not needed for session-level mask\n",
      "Sess01 Update not needed for run 005 mask\n",
      "Sess01 Update not needed for run 005 meanval\n",
      "Fri Nov 24 13:11:14 CET 2017\n",
      "mkbrainmask-sess done\n",
      "Sess01 MC -----------------------------\n",
      "mc-sess -fstem f -fmcstem fmcpr -s Sess01 -d /data/martin/prosopagnosia/hands -fsd bold -per-run -nolog -update\n",
      "Logfile is /dev/null\n",
      "-------------------------------------------\n",
      "/data/martin/prosopagnosia/hands/Sess01 \n",
      "RunList: 005\n",
      "Sess01 005 Update not needed\n",
      "\n",
      "\n",
      "Fri Nov 24 13:11:14 CET 2017\n",
      "mc-sess completed SUCCESSFULLY\n",
      "Sess01 To Surface -----------------------------\n",
      "rawfunc2surf-sess -fwhm 5 -s Sess01 -d /data/martin/prosopagnosia/hands -fsd bold -hemi rh -trgsubject pBrain -nolog -update -per-run\n",
      "instem fmcpr\n",
      "outstem fmcpr.sm5.pBrain.hemi\n",
      "------------------------------ \n",
      "1/1 Sess01\n",
      "  1/1 Sess01 005 rh ---------\n",
      "    Fri Nov 24 13:11:14 CET 2017\n",
      "/data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.rh.pr.nii.gz does not need updating\n",
      "/data/martin/prosopagnosia/hands/Sess01/bold/masks/brain.pBrain.rh.pr.nii.gz does not need updating\n",
      "  1/1 Sess01 005 rh ---------\n",
      "    Fri Nov 24 13:11:14 CET 2017\n",
      "    Sess01 005 Update not needed\n",
      "\n",
      "Fri Nov 24 13:11:14 CET 2017\n",
      "rawfunc2surf-sess completed \n",
      "----------------------------------------\n",
      "Started at Fri Nov 24 13:11:14 CET 2017\n",
      "Ended   at Fri Nov 24 13:11:14 CET 2017\n",
      "preproc-sess done\n",
      "-------------------------------------------\n",
      "1/1 /data/martin/prosopagnosia/hands/Sess01 \n",
      "Fri Nov 24 13:11:15 CET 2017\n",
      "anadir = /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.rh\n",
      "DoGLMFit = 1\n",
      "DoContrasts = 1\n",
      "UpdateNeeded = 1\n",
      "    Sess01 Update needed\n",
      "/data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.rh/sxa3.config.txt\n",
      "MLF is /tmp/selxavg3-sess-29243.m\n",
      "------------------------------------------\n",
      "% Fri Nov 24 13:11:14 CET 2017  \n",
      "% /data/martin/prosopagnosia/hands  \n",
      "%  design.sm5.rh  \n",
      "which fast_selxavg3\n",
      "which fast_ldanaflac\n",
      "which MRIread\n",
      "  \n",
      "  \n",
      "fast_selxavg3b('/data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.rh/sxa3.config.txt')\n",
      "if(~fast_fileexists('/tmp/selxavg3-sess-29243.ok')); quit; end\n",
      "%--------------------------------\n",
      "  \n",
      "  \n",
      "quit;\n",
      "------------------------------------------\n",
      "------------------------------------------\n",
      "------- matlab output --------------------\n",
      "MATLAB is selecting SOFTWARE OPENGL rendering.\n",
      "\n",
      "                            < M A T L A B (R) >\n",
      "                  Copyright 1984-2016 The MathWorks, Inc.\n",
      "                   R2016a (9.0.0.341360) 64-bit (glnxa64)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "                             February 11, 2016\n",
      "\n",
      " \n",
      "To get started, type one of these: helpwin, helpdesk, or demo.\n",
      "For product information, visit www.mathworks.com.\n",
      " \n",
      "\n",
      "\tThis is a Classroom License for instructional use only.\n",
      "\tResearch and commercial use is prohibited.\n",
      "\n",
      ">> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m\n",
      ">> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m\n",
      ">> /usr/local/freesurfer/matlab/MRIread.m\n",
      ">> >> >> starting fast_selxavg3b\n",
      "\n",
      "\n",
      "#@# Sess01 ###############################\n",
      "/data/martin/prosopagnosia/hands/Sess01\n",
      "-------------------------\n",
      "$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $\n",
      "-------------------------\n",
      "outtop = /data/martin/prosopagnosia/hands\n",
      "Extension format = nii.gz\n",
      "INFO: key nSliceGroups unrecognized, line 11, skipping\n",
      " 1 act-vs-rest.mat\n",
      "nruns = 1\n",
      "autostimdur = \n",
      "\n",
      "\n",
      "outanadir = /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.rh\n",
      "parfiles condition id list:  1 \n",
      "Found 81954/111586 (73.4) voxels in mask 1\n",
      "Creating Design Matrix\n",
      " ... creation time =  0.002 sec\n",
      "DoMCFit = 1\n",
      "ntptot = 197, nX = 7, DOF = 190\n",
      "Saving X matrix to /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.rh/Xtmp.mat\n",
      "XCond = 6.16311 (normalized)\n",
      "Computing compensation for resdual AR1 bias\n",
      " 1  -0.5  -0.499068    (t=0.007273)\n",
      " 2  -0.25  -0.260307    (t=0.009316)\n",
      " 3  0  -0.0243493    (t=0.011247)\n",
      " 4  0.25  0.206065    (t=0.013042)\n",
      " 5  0.5  0.423608    (t=0.01797)\n",
      "AR1 Correction M: 0.0333089 1.08109\n",
      "Computing contrast matrices\n",
      "OLS Beta Pass \n",
      "  run 1    t= 0.0\n",
      "reading data ... 0.769529\n",
      "    Global Mean   824.69\n",
      "Global In-Mask Mean = 824.69 (814.787)\n",
      "Rescale Target = 100\n",
      "RescaleFactor = 0.121258\n",
      "OLS Residual Pass \n",
      "  run 1    t= 0.0\n",
      "reading data ... 0.79182\n",
      "Saving rho1\n",
      "Smoothing ACF\n",
      "/usr/local/freesurfer/bin/mris_fwhm --mask /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.rh/mask.nii.gz --i /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.rh/rho1mn.nii.gz --o /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.rh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s pBrain --hemi rh --sd /usr/local/freesurfer/subjects\n",
      "pBrain rh white\n",
      "Number of vertices 111586\n",
      "Number of faces    223168\n",
      "Total area         73917.976562\n",
      "GroupSurface 0\n",
      "AvgVtxArea       0.662431\n",
      "AvgVtxDist       0.889571\n",
      "StdVtxDist       0.264496\n",
      "Loading mask /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.rh/mask.nii.gz\n",
      "Found 81954 voxels in mask\n",
      "Not Polynomial detrending\n",
      "Smoothing input by fwhm=20.000000, gstd=8.493218, niters=223 \n",
      "Only smoothing, so saving and exiting now\n",
      "\n",
      "Found 0 voxels with corrected AR1 > 0.90\n",
      "Whitening\n",
      "Computing whitening matrices\n",
      "Alloc Sinv: 197 197 30 ...  done t = 0.001711 sec\n",
      "  seg   1   2732  nrho1 = 0.050\n",
      "  seg   2   2732  nrho1 = 0.066\n",
      "  seg   3   2732  nrho1 = 0.076\n",
      "  seg   4   2732  nrho1 = 0.084\n",
      "  seg   5   2732  nrho1 = 0.090\n",
      "  seg   6   2732  nrho1 = 0.096\n",
      "  seg   7   2732  nrho1 = 0.102\n",
      "  seg   8   2732  nrho1 = 0.109\n",
      "  seg   9   2732  nrho1 = 0.116\n",
      "  seg  10   2732  nrho1 = 0.122\n",
      "  seg  11   2732  nrho1 = 0.127\n",
      "  seg  12   2732  nrho1 = 0.133\n",
      "  seg  13   2732  nrho1 = 0.139\n",
      "  seg  14   2732  nrho1 = 0.146\n",
      "  seg  15   2732  nrho1 = 0.152\n",
      "  seg  16   2732  nrho1 = 0.156\n",
      "  seg  17   2732  nrho1 = 0.161\n",
      "  seg  18   2732  nrho1 = 0.166\n",
      "  seg  19   2732  nrho1 = 0.172\n",
      "  seg  20   2732  nrho1 = 0.179\n",
      "  seg  21   2732  nrho1 = 0.186\n",
      "  seg  22   2732  nrho1 = 0.194\n",
      "  seg  23   2732  nrho1 = 0.204\n",
      "  seg  24   2732  nrho1 = 0.216\n",
      "  seg  25   2732  nrho1 = 0.231\n",
      "  seg  26   2732  nrho1 = 0.252\n",
      "  seg  27   2732  nrho1 = 0.276\n",
      "  seg  28   2732  nrho1 = 0.298\n",
      "  seg  29   2732  nrho1 = 0.328\n",
      "  seg  30   2726  nrho1 = 0.361\n",
      "GLS Beta Pass \n",
      "  run 1    t= 0.0\n",
      "GLS Residual Pass \n",
      "  run 1    t= 0.0\n",
      "Found 29632 zero-valued voxels\n",
      "Computing contrasts\n",
      "Starting contrasts\n",
      "act-vs-rest J=1 -------------\n",
      "Saving efficiency 35.2096\n",
      "Testing Motion Correction Parameters\n",
      " -0.76  -0.06  -0.16   0.62  -0.18  -0.83  -0.16  -0.11  -0.17   0.79   0.44   0.39   0.03  -0.69  -0.16  -0.11   0.16   0.11 \n",
      "Saving h.dat to /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.rh/h.dat\n",
      "cputime-min 0.065833\n",
      "fast_selxavg3 done for /data/martin/prosopagnosia/hands/Sess01\n",
      "\n",
      "ans =\n",
      "\n",
      "     0\n",
      "\n",
      ">> >> >> >> >> ------------------------------------------\n",
      "Started at Fri Nov 24 13:11:14 CET 2017\n",
      "Ended   at Fri Nov 24 13:11:31 CET 2017\n",
      " \n",
      "selxavg3-sess completed\n",
      " \n",
      "Setting TER to 0.050000\n",
      "Setting TimeWindow to 40.000000\n",
      "Setting PreStim    to 0\n",
      "Setting PostStim   to 40.000000\n",
      "# FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c\n",
      "# MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $\n",
      "# MKACMD /usr/local/freesurfer/fsfast/bin/mkanalysis-sess -analysis design.sm5.lh -surface pBrain lh -per-run -fwhm 5 -fsd bold -paradigm design.par -event-related -spmhrf 0 -refeventdur 12 -polyfit 2 -mcextreg -nskip 0 -TR 3 -nconditions 1\n",
      "# DATE Fri Nov 24 13:11:31 CET 2017\n",
      "\n",
      "analysis design.sm5.lh\n",
      "mcstem fmcpr\n",
      "fsd bold\n",
      "TR 3\n",
      "RegDOF 6\n",
      "PerSession 0\n",
      "RawSpace surface pBrain lh\n",
      "mask brain\n",
      "RawFWHM 5\n",
      "RawSTC none\n",
      "nSliceGroups 1\n",
      "UseB0DC 0\n",
      "ApplySubCortMask 1\n",
      "inorm 100\n",
      "acfbins 30\n",
      "fixacf  1\n",
      "acffwhm 20\n",
      "acfsvd  0\n",
      "designtype event-related\n",
      "nskip 0\n",
      "polyfit 2\n",
      "HPFCutoffHz 0\n",
      "HeteroGCor 0\n",
      "nconditions 1\n",
      "parname design.par\n",
      "RefEventDur 12\n",
      "timewindow 40.000000\n",
      "prestim 0\n",
      "TER 0.050000\n",
      "spmhrf 0\n",
      "stimulusdelay -1.50000000000000000000\n",
      "Condition 1 Condition01\n",
      "nuisreg mcprextreg 3\n",
      "mkanalysis-sess done\n",
      "INFO: Found 1 Non-Null Conditions\n",
      "INFO: Found 1 Delays\n",
      "Condition Weights: 1.00000000000000000000\n",
      "mkcontrast2 -config design.sm5.lh/act-vs-rest.config -anadir design.sm5.lh -wcond 1.00000000000000000000 -sumconds -o design.sm5.lh/act-vs-rest.mat -wdelay 1 -no-octave\n",
      "  $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $\n",
      "cmtxfile  design.sm5.lh/act-vs-rest.mat\n",
      "nconds    1,  wcond  1.00000000000000000000\n",
      "ndelays   1, wdelay 1\n",
      "ndelays   1, wpsa   \n",
      "sumconds  1\n",
      "sumdelays 0\n",
      "nircorr   0\n",
      "TER       0.050000\n",
      "rdelta    \n",
      "rtau      \n",
      "  cmtxfile  design.sm5.lh/act-vs-rest.mat\n",
      "  monly  0\n",
      "  NCond   1\n",
      "  WCond   1.00000000000000000000\n",
      "  NDelay  1\n",
      "  WDelay  1\n",
      "  TER         0.050000\n",
      "  sumconds   1\n",
      "  sumdelays  0\n",
      "  nircorr  0\n",
      "  TPreStim  0\n",
      "  RmPreStim  0\n",
      "  rdelta     0 0\n",
      "  rtau       0 0\n",
      "  ndelays    1\n",
      "  CNorm      1\n",
      "  setwdelay  0\n",
      "  setwcond   0\n",
      "Matlab file is /tmp/mkcontrast2.30652.m\n",
      "MATLAB is selecting SOFTWARE OPENGL rendering.\n",
      "\n",
      "                            < M A T L A B (R) >\n",
      "                  Copyright 1984-2016 The MathWorks, Inc.\n",
      "                   R2016a (9.0.0.341360) 64-bit (glnxa64)\n",
      "                             February 11, 2016\n",
      "\n",
      " \n",
      "To get started, type one of these: helpwin, helpdesk, or demo.\n",
      "For product information, visit www.mathworks.com.\n",
      " \n",
      "\n",
      "\tThis is a Classroom License for instructional use only.\n",
      "\tResearch and commercial use is prohibited.\n",
      "\n",
      ">> starting mkcontrast2m\n",
      "Normalizing contrast matrix\n",
      "mkcontrast2m done\n",
      ">> Fri Nov 24 13:11:39 CET 2017\n",
      "Surface data pBrain lh\n",
      "--------------------------------------------------------------\n",
      "selxavg3-sess logfile is /data/martin/prosopagnosia/hands/log/selxavg3-sess-bold-design.sm5.lh-171124131139.log\n",
      "--------------------------------------------------------------\n",
      "selxavg3-sess log file\n",
      "/usr/local/freesurfer/fsfast/bin/selxavg3-sess\n",
      "-sf sessids -analysis design.sm5.lh\n",
      "$Id: selxavg3-sess,v 1.68 2016/05/10 03:24:18 greve Exp $\n",
      "uid=1000(martin) gid=1000(martin) groups=1000(martin),24(cdrom),25(floppy),29(audio),30(dip),44(video),46(plugdev),108(netdev),110(lpadmin),113(scanner),117(bluetooth),999(docker)\n",
      "/data/martin/prosopagnosia/hands\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "Fri Nov 24 13:11:39 CET 2017\n",
      "preproc-sess -s Sess01 -d /data/martin/prosopagnosia/hands -a design.sm5.lh -nolog\n",
      "--------------------------------------------------------------\n",
      "preproc-sess logfile is /dev/null\n",
      "--------------------------------------------------------------\n",
      "$Id: preproc-sess,v 1.64.2.1 2016/08/02 21:19:09 greve Exp $\n",
      "martin\n",
      "setenv FREESURFER_HOME /usr/local/freesurfer\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "/data/martin/prosopagnosia/hands\n",
      "/usr/local/freesurfer/fsfast/bin/preproc-sess\n",
      "-s Sess01 -d /data/martin/prosopagnosia/hands -a design.sm5.lh -nolog\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Fri Nov 24 13:11:39 CET 2017\n",
      "instem   f \n",
      "mc   1     f fmcpr \n",
      "stc  0     fmcpr\n",
      "sm   0   \n",
      "mask 1   brain\n",
      "Sess01 Template -----------------------------\n",
      "mktemplate-sess -s Sess01 -d /data/martin/prosopagnosia/hands -fsd bold -nolog -update\n",
      " \n",
      "Session: /data/martin/prosopagnosia/hands/Sess01 ----------------\n",
      "Fri Nov 24 13:11:39 CET 2017\n",
      "Detected input format at nii\n",
      "Sess01 Update not needed\n",
      "  Run: 005 ----------------\n",
      "  Fri Nov 24 13:11:39 CET 2017\n",
      "  Sess01 005 Update not needed\n",
      "Fri Nov 24 13:11:39 CET 2017\n",
      "mktemplate-sess completed \n",
      "Sess01 Registration -----------------------------\n",
      "register-sess -s Sess01 -d /data/martin/prosopagnosia/hands -fsd bold -delete-dat -dof 6 -bold -per-run -nolog -update -init-coreg\n",
      "--------------------------------------------------------------\n",
      "register-sess logfile is /dev/null\n",
      "--------------------------------------------------------------\n",
      "Fri Nov 24 13:11:39 CET 2017\n",
      "\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "cd /data/martin/prosopagnosia/hands\n",
      "/usr/local/freesurfer/fsfast/bin/register-sess -s Sess01 -d /data/martin/prosopagnosia/hands -fsd bold -delete-dat -dof 6 -bold -per-run -nolog -update -init-coreg\n",
      "\n",
      "freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      " \n",
      "Session: /data/martin/prosopagnosia/hands/Sess01 ----------------\n",
      "Fri Nov 24 13:11:39 CET 2017\n",
      "/data/martin/prosopagnosia/hands/Sess01\n",
      "  Run: 005 ----------------\n",
      "Fri Nov 24 13:11:39 CET 2017\n",
      "Update not needed\n",
      "Fri Nov 24 13:11:39 CET 2017\n",
      "register-sess completed \n",
      "Sess01 Mask ------------------------\n",
      "mkbrainmask-sess -maskstem brain -fsd bold -s Sess01 -d /data/martin/prosopagnosia/hands -per-run -nolog -update\n",
      "------------------------------------------------\n",
      "/data/martin/prosopagnosia/hands/Sess01 \n",
      "Fri Nov 24 13:11:39 CET 2017\n",
      "Sess01 Update not needed for session-level mask\n",
      "Sess01 Update not needed for run 005 mask\n",
      "Sess01 Update not needed for run 005 meanval\n",
      "Fri Nov 24 13:11:39 CET 2017\n",
      "mkbrainmask-sess done\n",
      "Sess01 MC -----------------------------\n",
      "mc-sess -fstem f -fmcstem fmcpr -s Sess01 -d /data/martin/prosopagnosia/hands -fsd bold -per-run -nolog -update\n",
      "Logfile is /dev/null\n",
      "-------------------------------------------\n",
      "/data/martin/prosopagnosia/hands/Sess01 \n",
      "RunList: 005\n",
      "Sess01 005 Update not needed\n",
      "\n",
      "\n",
      "Fri Nov 24 13:11:39 CET 2017\n",
      "mc-sess completed SUCCESSFULLY\n",
      "Sess01 To Surface -----------------------------\n",
      "rawfunc2surf-sess -fwhm 5 -s Sess01 -d /data/martin/prosopagnosia/hands -fsd bold -hemi lh -trgsubject pBrain -nolog -update -per-run\n",
      "instem fmcpr\n",
      "outstem fmcpr.sm5.pBrain.hemi\n",
      "------------------------------ \n",
      "1/1 Sess01\n",
      "  1/1 Sess01 005 lh ---------\n",
      "    Fri Nov 24 13:11:39 CET 2017\n",
      "/data/martin/prosopagnosia/hands/Sess01/bold/005/masks/brain.pBrain.lh.pr.nii.gz does not need updating\n",
      "/data/martin/prosopagnosia/hands/Sess01/bold/masks/brain.pBrain.lh.pr.nii.gz does not need updating\n",
      "  1/1 Sess01 005 lh ---------\n",
      "    Fri Nov 24 13:11:39 CET 2017\n",
      "    Sess01 005 Update not needed\n",
      "\n",
      "Fri Nov 24 13:11:39 CET 2017\n",
      "rawfunc2surf-sess completed \n",
      "----------------------------------------\n",
      "Started at Fri Nov 24 13:11:39 CET 2017\n",
      "Ended   at Fri Nov 24 13:11:39 CET 2017\n",
      "preproc-sess done\n",
      "-------------------------------------------\n",
      "1/1 /data/martin/prosopagnosia/hands/Sess01 \n",
      "Fri Nov 24 13:11:39 CET 2017\n",
      "anadir = /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.lh\n",
      "DoGLMFit = 1\n",
      "DoContrasts = 1\n",
      "UpdateNeeded = 1\n",
      "    Sess01 Update needed\n",
      "/data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.lh/sxa3.config.txt\n",
      "MLF is /tmp/selxavg3-sess-31002.m\n",
      "------------------------------------------\n",
      "% Fri Nov 24 13:11:39 CET 2017  \n",
      "% /data/martin/prosopagnosia/hands  \n",
      "%  design.sm5.lh  \n",
      "which fast_selxavg3\n",
      "which fast_ldanaflac\n",
      "which MRIread\n",
      "  \n",
      "  \n",
      "fast_selxavg3b('/data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.lh/sxa3.config.txt')\n",
      "if(~fast_fileexists('/tmp/selxavg3-sess-31002.ok')); quit; end\n",
      "%--------------------------------\n",
      "  \n",
      "  \n",
      "quit;\n",
      "------------------------------------------\n",
      "------------------------------------------\n",
      "------- matlab output --------------------\n",
      "MATLAB is selecting SOFTWARE OPENGL rendering.\n",
      "\n",
      "                            < M A T L A B (R) >\n",
      "                  Copyright 1984-2016 The MathWorks, Inc.\n",
      "                   R2016a (9.0.0.341360) 64-bit (glnxa64)\n",
      "                             February 11, 2016\n",
      "\n",
      " \n",
      "To get started, type one of these: helpwin, helpdesk, or demo.\n",
      "For product information, visit www.mathworks.com.\n",
      " \n",
      "\n",
      "\tThis is a Classroom License for instructional use only.\n",
      "\tResearch and commercial use is prohibited.\n",
      "\n",
      ">> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m\n",
      ">> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m\n",
      ">> /usr/local/freesurfer/matlab/MRIread.m\n",
      ">> >> >> starting fast_selxavg3b\n",
      "\n",
      "\n",
      "#@# Sess01 ###############################\n",
      "/data/martin/prosopagnosia/hands/Sess01\n",
      "-------------------------\n",
      "$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $\n",
      "-------------------------\n",
      "outtop = /data/martin/prosopagnosia/hands\n",
      "Extension format = nii.gz\n",
      "INFO: key nSliceGroups unrecognized, line 11, skipping\n",
      " 1 act-vs-rest.mat\n",
      "nruns = 1\n",
      "autostimdur = \n",
      "\n",
      "\n",
      "outanadir = /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.lh\n",
      "parfiles condition id list:  1 \n",
      "Found 82533/112635 (73.3) voxels in mask 1\n",
      "Creating Design Matrix\n",
      " ... creation time =  0.002 sec\n",
      "DoMCFit = 1\n",
      "ntptot = 197, nX = 7, DOF = 190\n",
      "Saving X matrix to /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.lh/Xtmp.mat\n",
      "XCond = 6.16311 (normalized)\n",
      "Computing compensation for resdual AR1 bias\n",
      " 1  -0.5  -0.499068    (t=0.007441)\n",
      " 2  -0.25  -0.260307    (t=0.0097)\n",
      " 3  0  -0.0243493    (t=0.012734)\n",
      " 4  0.25  0.206065    (t=0.015495)\n",
      " 5  0.5  0.423608    (t=0.022419)\n",
      "AR1 Correction M: 0.0333089 1.08109\n",
      "Computing contrast matrices\n",
      "OLS Beta Pass \n",
      "  run 1    t= 0.0\n",
      "reading data ... 0.775603\n",
      "    Global Mean   824.69\n",
      "Global In-Mask Mean = 824.69 (849.538)\n",
      "Rescale Target = 100\n",
      "RescaleFactor = 0.121258\n",
      "OLS Residual Pass \n",
      "  run 1    t= 0.0\n",
      "reading data ... 0.802061\n",
      "Saving rho1\n",
      "Smoothing ACF\n",
      "/usr/local/freesurfer/bin/mris_fwhm --mask /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.lh/mask.nii.gz --i /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.lh/rho1mn.nii.gz --o /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.lh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s pBrain --hemi lh --sd /usr/local/freesurfer/subjects\n",
      "pBrain lh white\n",
      "Number of vertices 112635\n",
      "Number of faces    225266\n",
      "Total area         74093.468750\n",
      "GroupSurface 0\n",
      "AvgVtxArea       0.657819\n",
      "AvgVtxDist       0.887337\n",
      "StdVtxDist       0.259981\n",
      "Loading mask /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.lh/mask.nii.gz\n",
      "Found 82533 voxels in mask\n",
      "Not Polynomial detrending\n",
      "Smoothing input by fwhm=20.000000, gstd=8.493218, niters=224 \n",
      "Only smoothing, so saving and exiting now\n",
      "\n",
      "Found 0 voxels with corrected AR1 > 0.90\n",
      "Whitening\n",
      "Computing whitening matrices\n",
      "Alloc Sinv: 197 197 30 ...  done t = 0.001261 sec\n",
      "  seg   1   2751  nrho1 = 0.058\n",
      "  seg   2   2751  nrho1 = 0.075\n",
      "  seg   3   2751  nrho1 = 0.084\n",
      "  seg   4   2751  nrho1 = 0.092\n",
      "  seg   5   2751  nrho1 = 0.100\n",
      "  seg   6   2751  nrho1 = 0.108\n",
      "  seg   7   2751  nrho1 = 0.113\n",
      "  seg   8   2751  nrho1 = 0.119\n",
      "  seg   9   2751  nrho1 = 0.124\n",
      "  seg  10   2751  nrho1 = 0.129\n",
      "  seg  11   2751  nrho1 = 0.134\n",
      "  seg  12   2751  nrho1 = 0.141\n",
      "  seg  13   2751  nrho1 = 0.147\n",
      "  seg  14   2751  nrho1 = 0.153\n",
      "  seg  15   2751  nrho1 = 0.160\n",
      "  seg  16   2751  nrho1 = 0.167\n",
      "  seg  17   2751  nrho1 = 0.175\n",
      "  seg  18   2751  nrho1 = 0.184\n",
      "  seg  19   2751  nrho1 = 0.194\n",
      "  seg  20   2751  nrho1 = 0.203\n",
      "  seg  21   2751  nrho1 = 0.212\n",
      "  seg  22   2751  nrho1 = 0.222\n",
      "  seg  23   2751  nrho1 = 0.233\n",
      "  seg  24   2751  nrho1 = 0.245\n",
      "  seg  25   2751  nrho1 = 0.259\n",
      "  seg  26   2751  nrho1 = 0.274\n",
      "  seg  27   2751  nrho1 = 0.291\n",
      "  seg  28   2751  nrho1 = 0.308\n",
      "  seg  29   2751  nrho1 = 0.328\n",
      "  seg  30   2754  nrho1 = 0.375\n",
      "GLS Beta Pass \n",
      "  run 1    t= 0.0\n",
      "GLS Residual Pass \n",
      "  run 1    t= 0.0\n",
      "Found 30102 zero-valued voxels\n",
      "Computing contrasts\n",
      "Starting contrasts\n",
      "act-vs-rest J=1 -------------\n",
      "Saving efficiency 35.2096\n",
      "Testing Motion Correction Parameters\n",
      " -0.76  -0.06  -0.16   0.62  -0.18  -0.83  -0.16  -0.11  -0.17   0.79   0.44   0.39   0.03  -0.69  -0.16  -0.11   0.16   0.11 \n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Saving h.dat to /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.lh/h.dat\n",
      "cputime-min 0.066000\n",
      "fast_selxavg3 done for /data/martin/prosopagnosia/hands/Sess01\n",
      "\n",
      "ans =\n",
      "\n",
      "     0\n",
      "\n",
      ">> >> >> >> >> ------------------------------------------\n",
      "Started at Fri Nov 24 13:11:39 CET 2017\n",
      "Ended   at Fri Nov 24 13:11:57 CET 2017\n",
      " \n",
      "selxavg3-sess completed\n",
      " \n"
     ]
    }
   ],
   "source": [
    "for hemi in \"rh\" \"lh\"; do\n",
    "\n",
    "    mkanalysis-sess -analysis design.sm5.${hemi} \\\n",
    "    -surface pBrain ${hemi} \\\n",
    "    -per-run \\\n",
    "    -fwhm 5 \\\n",
    "    -fsd bold \\\n",
    "    -paradigm design.par \\\n",
    "    -event-related \\\n",
    "    -spmhrf 0 \\\n",
    "    -refeventdur 12 \\\n",
    "    -polyfit 2 \\\n",
    "    -mcextreg \\\n",
    "    -nskip 0 \\\n",
    "    -TR 3 \\\n",
    "    -nconditions 1\n",
    "\n",
    "    mkcontrast-sess -analysis design.sm5.${hemi} -contrast act-vs-rest -a 1 -c 0\n",
    "\n",
    "    selxavg3-sess -sf sessids -analysis design.sm5.${hemi}\n",
    "\n",
    "done"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Surface pBrain lh\n",
      "Map Surface pBrain lh\n",
      "$Id: tksurfer-sess,v 1.26 2015/12/10 22:51:31 zkaufman Exp $\n",
      "Linux dhcp-129-70-100-154 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2 (2016-04-08) x86_64 GNU/Linux\n",
      "Fri Nov 24 13:12:49 CET 2017\n",
      "/usr/local/freesurfer/bin/tksurfer\n",
      "\n",
      "list act-vs-rest\n",
      "con/map act-vs-rest /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.lh/act-vs-rest/t.nii.gz\n",
      "maplist /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.lh/act-vs-rest/t.nii.gz\n",
      "mri_concat /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.lh/act-vs-rest/t.nii.gz --o /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.lh/tksconcat.nii\n",
      "ninputs = 1\n",
      "Checking inputs\n",
      "nframestot = 1\n",
      "Allocing output\n",
      "Done allocing\n",
      "nframes = 1\n",
      "Writing to /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.lh/tksconcat.nii\n",
      "cd /data/martin/prosopagnosia/hands\n",
      "setenv SUBJECTS_DIR /usr/local/freesurfer/subjects\n",
      "tksurferfv pBrain lh inflated -overlay /data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.lh/tksconcat.nii -annot aparc -surf white -surf pial -fminmax 3 10\n",
      "\n",
      "Contrasts\n",
      "0 act-vs-rest\n",
      "\n",
      "\n",
      "freeview -f /usr/local/freesurfer/subjects/pBrain/surf/lh.pial:curvature=/usr/local/freesurfer/subjects/pBrain/surf/lh.curv:visible=0:annot=/usr/local/freesurfer/subjects/pBrain/label/lh.aparc.annot:edgethickness=0:annot_outline=1:overlay=/data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.lh/tksconcat.nii:overlay_threshold=3,10 /usr/local/freesurfer/subjects/pBrain/surf/lh.white:curvature=/usr/local/freesurfer/subjects/pBrain/surf/lh.curv:visible=0:annot=/usr/local/freesurfer/subjects/pBrain/label/lh.aparc.annot:edgethickness=0:annot_outline=1:overlay=/data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.lh/tksconcat.nii:overlay_threshold=3,10 /usr/local/freesurfer/subjects/pBrain/surf/lh.inflated:curvature=/usr/local/freesurfer/subjects/pBrain/surf/lh.curv:annot=/usr/local/freesurfer/subjects/pBrain/label/lh.aparc.annot:edgethickness=0:annot_outline=1:overlay=/data/martin/prosopagnosia/hands/Sess01/bold/design.sm5.lh/tksconcat.nii:overlay_threshold=3,10 -viewport 3d\n",
      "reading colortable from annotation file...\n",
      "colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)\n",
      "colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)\n",
      "reading colortable from annotation file...\n",
      "colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)\n",
      "colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)\n",
      "reading colortable from annotation file...\n",
      "colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)\n",
      "colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)\n",
      "Number of vertices in overlay data does not match with surface.\n"
     ]
    }
   ],
   "source": [
    "#tksurfer-sess -s Sess01 -analysis design.sm5.${hemi} -hemi ${hemi} -c act-vs-rest -map t -fthresh 3 -fmax 10"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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