Transmit bias pipeline

Examples/Scripts/TransmitBiasBatch.sh

@@ -0,0 +1,185 @@
+#!/bin/bash
+set -eu
+
+#environment configuration
+queue="long.q"
+EnvironmentScript="${HOME}/projects/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh" #Pipeline environment script
+
+#data location
+#DISCUSS: should this be "sessions"?  other batch scripts use subjects, but...
+subjects=(123456 654321)
+StudyFolder="${HOME}/projects/YA_HCP_Final"
+GroupName="HCP_S1200"
+
+#general settings
+#identifier for the subset of subjects that have transmit field scans
+#pseudotransmit doesn't have subject exclusion logic, or if you otherwise have made sure the entire group has good transmit data, you may want to set it equal to the group folder name
+partialname=Partial
+#partialname="$GroupName"
+#set this to a text file that has the scanner transmit voltages for all subjects in the provided list, in order
+VoltagesFile="$StudyFolder"/"$GroupName"/Scripts/Voltages.txt
+GradientDistortionCoeffs=
+RegName=MSMAll
+LowResMesh=32
+grayordRes=2
+transmitRes="$grayordRes"
+MyelinMappingFWHM=5
+oldMyelinMapping=FALSE
+#0 for compiled, 1 for interpreted, 2 for octave
+MatlabMode=0
+
+#transmit field acquisition details
+#mode must be AFI, B1Tx, or PseudoTransmit
+mode="AFI"
+#mode="B1Tx"
+#mode="PseudoTransmit"
+
+#AFI-specific settings
+AFITRone=20
+AFITRtwo=120
+AFITargetFlipAngle=50
+
+#B1Tx-specific settings
+#the value in the phase image where the flip angle was ideal
+B1TxPhaseDivisor=800
+
+#PseudoTransmit-specific settings
+fMRINames=rfMRI_REST1_AP@rfMRI_REST1_PA
+ptbbrthresh=0.5
+#set this to an already transmit-corrected group average myelin map
+ReferenceTemplate=
+
+#ALSO, edit the input filenames inside the first loop below
+
+#probably shouldn't edit this stuff
+if [[ "$RegName" == "" || "$RegName" == "MSMSulc" ]]
+then
+    RegStr=""
+else
+    RegStr="_$RegName"
+fi
+GMWMtemplate="$StudyFolder"/"$GroupName"/MNINonLinear/GMWMTemplate.nii.gz
+GroupCorrected="$StudyFolder"/"$GroupName"/MNINonLinear/fsaverage_LR"$LowResMesh"k/"$partialname".MyelinMap_GroupCorr"$RegStr"."$LowResMesh"k_fs_LR.dscalar.nii
+GroupUncorrectedMyelin="$StudyFolder"/"$GroupName"/MNINonLinear/fsaverage_LR"$LowResMesh"k/"$partialname".MyelinMap"$RegStr"."$LowResMesh"k_fs_LR.dscalar.nii
+#DISCUSS: not sure if external users need to generate this
+AllSubjUncorrected="$StudyFolder"/"$GroupName"/MNINonLinear/fsaverage_LR"$LowResMesh"k/"$partialname".All.MyelinMap"$RegStr"."$LowResMesh"k_fs_LR.dscalar.nii
+PTRefValFile="$StudyFolder"/"$GroupName"/PT_refval.txt
+
+source "$EnvironmentScript"
+
+phase1jobids=()
+for subject in "${subjects[@]}"
+do
+    #AFI-specific per-subject filenames
+    AFIImage=
+
+    #B1Tx-specific per-subject filenames
+    B1TxMag=
+    B1TxPhase=
+
+    #Receive bias inputs - ignore this if you used pre-scan normalize or similar
+    #unprocessed T1w and T2w are required to do receive correction
+    T1wUnprocList=
+    T2wUnprocList=
+    #use these two if you separately acquired bodycoil and headcoil images
+    BodyCoilImage=
+    HeadCoilImage=
+    #use these two if you acquired a PSN T1w and also saved its non-PSN reconstruction (but all the other raw image inputs are non-PSN)
+    rawT1wPSN=
+    rawT1wNoPSN=
+
+    phase1jobids+=($(fsl_sub -q "$queue" "$HCPPIPEDIR"/TransmitBias/Phase1_IndividualAlign.sh \
+        --study-folder="$StudyFolder" \
+        --subject="$subject" \
+        --mode="$mode" \
+        --afi-image="$AFIImage" \
+        --afi-tr-one="$AFITRone" \
+        --afi-tr-two="$AFITRtwo" \
+        --b1tx-magnitude="$B1TxMag" \
+        --b1tx-phase="$B1TxPhase" \
+        --b1tx-phase-divisor="$B1TxPhaseDivisor" \
+        --pt-fmri-names="$fMRINames" \
+        --pt-bbr-threshold="$ptbbrthresh" \
+        --unproc-t1w-list="$T1wUnprocList" \
+        --unproc-t2w-list="$T2wUnprocList" \
+        --receive-bias-body-coil="$BodyCoilImage" \
+        --receive-bias-head-coil="$HeadCoilImage" \
+        --raw-psn-t1w="$rawT1wPSN" \
+        --raw-nopsn-t1w="$rawT1wNoPSN" \
+        --scanner-grad-coeffs="$GradientDistortionCoeffs" \
+        --reg-name="$RegName" \
+        --low-res-mesh="$LowResMesh" \
+        --grayordinates-res="$grayordRes" \
+        --transmit-res="$transmitRes" \
+        --myelin-mapping-fwhm="$MyelinMappingFWHM" \
+        --old-myelin-mapping="$oldMyelinMapping"))
+done
+
+subjectsStr=$(IFS='@'; echo "${subjects[*]}")
+useRCFiles=FALSE
+if [[ "$T1wUnprocList" != "" ]]
+then
+    useRCFiles=TRUE
+fi
+
+mkdir -p "$StudyFolder"/"$GroupName"
+
+phase1jobstr=$(IFS=','; echo "${phase1jobids[*]}")
+phase2job=$(fsl_sub -q "$queue" -j "$phase1jobstr" "$HCPPIPEDIR"/TransmitBias/Phase2_GroupAverageFit.sh \
+    --study-folder="$StudyFolder" \
+    --subject-list="$subjectsStr" \
+    --mode="$mode" \
+    --group-average-name="$GroupName" \
+    --transmit-group-name="$partialname" \
+    --manual-receive="$useRCFiles" \
+    --gmwm-template-out="$GMWMtemplate" \
+    --average-myelin-out="$GroupUncorrectedMyelin" \
+    --all-myelin-out="$AllSubjUncorrected" \
+    --afi-tr-one="$AFITRone" \
+    --afi-tr-two="$AFITRtwo" \
+    --afi-angle="$AFITargetFlipAngle" \
+    --reference-value-out="$PTRefValFile" \
+    --reg-name="$RegName" \
+    --low-res-mesh="$LowResMesh" \
+    --grayordinates-res="$grayordRes" \
+    --matlab-run-mode="$MatlabMode")
+
+phase3jobids=()
+for subject in "${subjects[@]}"
+do
+    phase3jobids+=($(fsl_sub -q "$queue" -j "$phase2job" "$HCPPIPEDIR"/TransmitBias/Phase3_IndividualAdjustment.sh \
+        --study-folder="$StudyFolder" \
+        --subject="$subject" \
+        --mode="$mode" \
+        --manual-receive="$useRCFiles" \
+        --gmwm-template="$GMWMtemplate" \
+        --afi-tr-one="$AFITRone" \
+        --afi-tr-two="$AFITRtwo" \
+        --afi-angle="$AFITargetFlipAngle" \
+        --group-corrected-myelin="$GroupCorrected" \
+        --myelin-template="$ReferenceTemplate" \
+        --group-uncorrected-myelin="$GroupUncorrectedMyelin" \
+        --pt-reference-value-file="$PTRefValFile" \
+        --reg-name="$RegName" \
+        --low-res-mesh="$LowResMesh" \
+        --grayordinates-res="$grayordRes" \
+        --transmit-res="$transmitRes" \
+        --matlab-run-mode="$MatlabMode"))
+done
+
+phase3jobstr=$(IFS=','; echo "${phase3jobids[*]}")
+fsl_sub -q "$queue" -j "$phase3jobstr" "$HCPPIPEDIR"/TransmitBias/Phase4_GroupAverageCorrectedMaps.sh \
+    --study-folder="$StudyFolder" \
+    --subject-list="$subjectsStr" \
+    --mode="$mode" \
+    --group-average-name="$GroupName" \
+    --transmit-group-name="$partialname" \
+    --voltages="$VoltagesFile" \
+    --afi-tr-one="$AFITRone" \
+    --afi-tr-two="$AFITRtwo" \
+    --afi-angle="$AFITargetFlipAngle" \
+    --average-myelin="$GroupUncorrectedMyelin" \
+    --reg-name="$RegName" \
+    --low-res-mesh="$LowResMesh" \
+    --matlab-run-mode="$MatlabMode"
+

PostFreeSurfer/PostFreeSurferPipeline.sh

@@ -73,17 +73,13 @@ PARAMETERs are [ ] = optional; < > = user supplied value
 
 defaultSigma=$(echo "sqrt(200)" | bc -l)
 
-#arguments to opts_Add*: switch, variable to set, name for inside of <> in help text, description, [default value if AddOptional], [compatibility flag, ...]
-#help info for option gets printed like "--foo=<$3> - $4"
-
-#TSC:should --path or --study-folder be the flag displayed by the usage?
 opts_AddMandatory '--study-folder' 'StudyFolder' 'path' "folder containing all subjects" "--path"
 opts_AddMandatory '--session' 'Session' 'session ID' "session (timepoint, visit) label." "--subject" #legacy --subject option
-opts_AddMandatory '--surfatlasdir' 'SurfaceAtlasDIR' 'path' "<HCPpipelines>/global/templates/standard_mesh_atlases or equivalent"
-opts_AddMandatory '--grayordinatesres' 'GrayordinatesResolutions' 'number' "usually '2', resolution of grayordinates to use"
-opts_AddMandatory '--grayordinatesdir' 'GrayordinatesSpaceDIR' 'path' "<HCPpipelines>/global/templates/<num>_Greyordinates or equivalent, for the given --grayordinatesres"
-opts_AddMandatory '--hiresmesh' 'HighResMesh' 'number' "usually '164', the standard mesh for T1w-resolution data data"
-opts_AddMandatory '--lowresmesh' 'LowResMeshes' 'number' "usually '32', the standard mesh for fMRI data"
+opts_AddOptional '--surfatlasdir' 'SurfaceAtlasDIR' 'path' "path to find low resolution spheres, etc, default <pipelines>/global/templates/standard_mesh_atlases" "$HCPPIPEDIR/global/templates/standard_mesh_atlases"
+opts_AddOptional '--grayordinatesres' 'GrayordinatesResolution' 'number' "resolution of grayordinates to use, default 2" '2'
+opts_AddOptional '--grayordinatesdir' 'GrayordinatesSpaceDIR' 'path' "<pipelines>/global/templates/<num>_Greyordinates or equivalent, for the given --grayordinatesres"
+opts_AddOptional '--hiresmesh' 'HighResMesh' 'number' "the standard mesh for T1w-resolution data data, default 164" '164'
+opts_AddOptional '--lowresmesh' 'LowResMeshes' 'number' "the standard mesh(es) to use for fMRI data, like 32@59"
 opts_AddMandatory '--subcortgraylabels' 'SubcorticalGrayLabels' 'file' "location of FreeSurferSubcorticalLabelTableLut.txt"
 opts_AddMandatory '--freesurferlabels' 'FreeSurferLabels' 'file' "location of FreeSurferAllLut.txt"
 opts_AddMandatory '--refmyelinmaps' 'ReferenceMyelinMaps' 'file' "group myelin map to use for bias correction"
@@ -129,6 +125,38 @@ fi
 #display the parsed/default values
 opts_ShowValues
 
+#internal scripts don't actually support multiple low res in one call, mostly because they are in different folders
+if [[ "$GrayordinatesSpaceDIR" == "" ]]
+then
+    case "$GrayordinatesResolution" in
+        (2)
+            GrayordinatesSpaceDIR="$HCPPIPEDIR"/global/templates/91282_Greyordinates
+            ;;
+        (1.60)
+            GrayordinatesSpaceDIR="$HCPPIPEDIR"/global/templates/170494_Greyordinates
+            ;;
+        (*)
+            log_Err_Abort "grayordinate resolution '$GrayordinatesResolution' not recognized as a standard resolution, please use '2', '1.60', or specify --grayordinatesdir manually"
+            ;;
+    esac
+fi
+
+#internal scripts do support lists for this LowResMeshes though...
+if [[ "$LowResMeshes" == "" ]]
+then
+    case "$GrayordinatesResolution" in
+        (2)
+            LowResMeshes=32
+            ;;
+        (1.60)
+            LowResMeshes=59
+            ;;
+        (*)
+            log_Err_Abort "grayordinate resolution '$GrayordinatesResolution' not recognized as a standard resolution, please use '2', '1.60', or specify --lowresmesh manually"
+            ;;
+    esac
+fi
+
 doProcessing=1
 doQC=1
 
@@ -306,7 +334,7 @@ if ((doProcessing)); then
     argList+=("$T1wImageBrainMask")         # ${17}
     argList+=("$FreeSurferLabels")          # ${18}
     argList+=("$GrayordinatesSpaceDIR")     # ${19}
-    argList+=("$GrayordinatesResolutions")  # ${20}
+    argList+=("$GrayordinatesResolution")   # ${20}
     argList+=("$SubcorticalGrayLabels")     # ${21}
     argList+=("$RegName")                   # ${22}
     argList+=("$InflateExtraScale")         # ${23}