fMRIVolume Related Pull Request — Use of a specific BOLD mask

fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh

@@ -24,6 +24,8 @@ fi
 
 source $HCPPIPEDIR/global/scripts/log.shlib  # Logging related functions
 source $HCPPIPEDIR/global/scripts/opts.shlib # Command line option functions
+source ${HCPPIPEDIR}/global/scripts/processingmodecheck.shlib  # Check processing mode requirements
+
 
 ################################################ SUPPORT FUNCTIONS ##################################################
 
@@ -220,6 +222,43 @@ then
 	log_Err_Abort "the --usejacobian option must be 'true' or 'false'"
 fi
 
+
+# ------------------------------------------------------------------------------
+#  Legacy Style Data Options
+# ------------------------------------------------------------------------------
+
+BOLDMask=`opts_GetOpt1 "--boldmask" $@`                                   # Specifies what mask to use for the final bold:
+                                                                          #   T1_fMRI_FOV: combined T1w brain mask and fMRI FOV masks (the default), 
+                                                                          #   T1_DILATED_fMRI_FOV: a once dilated T1w brain based mask combined with fMRI FOV
+                                                                          #   T1_DILATED2x_fMRI_FOV: a twice dilated T1w brain based mask combined with fMRI FOV, 
+                                                                          #   fMRI_FOV: a fMRI FOV mask
+
+# Defaults
+BOLDMask=`opts_DefaultOpt $BOLDMask "T1_fMRI_FOV"`
+
+# ------------------------------------------------------------------------------
+#  Compliance check
+# ------------------------------------------------------------------------------
+
+ProcessingMode=`opts_GetOpt1 "--processing-mode" $@`
+ProcessingMode=`opts_DefaultOpt $ProcessingMode "HCPStyleData"`
+Compliance="HCPStyleData"
+ComplianceMsg=""
+
+if [ "${BOLDMask}" != 'T1_fMRI_FOV' ]; then
+  if [ "${BOLDMask}" != "T1_DILATED_fMRI_FOV" ] && [ "${BOLDMask}" != "T1_DILATED2x_fMRI_FOV" ] && [ "${BOLDMask}" != "fMRI_FOV" ] ; then
+    log_Err_Abort "--boldmask=${BOLDMask} is invalid! Valid options are: T1_fMRI_FOV (default), T1_DILATED_fMRI_FOV, T1_DILATED2x_fMRI_FOV, fMRI_FOV."
+  fi
+  ComplianceMsg+=" --boldmask=${BOLDMask}"
+  Compliance="LegacyStyleData"
+fi
+
+check_mode_compliance "${ProcessingMode}" "${Compliance}" "${ComplianceMsg}"
+
+# -- End compliance check
+
+
+
 # Setup PATHS
 PipelineScripts=${HCPPIPEDIR_fMRIVol}
 GlobalScripts=${HCPPIPEDIR_Global}
@@ -461,7 +500,8 @@ ${RUN} ${PipelineScripts}/IntensityNormalization.sh \
        --ofmri=${fMRIFolder}/${NameOffMRI}_nonlin_norm \
        --inscout=${fMRIFolder}/${NameOffMRI}_SBRef_nonlin \
        --oscout=${fMRIFolder}/${NameOffMRI}_SBRef_nonlin_norm \
-       --usejacobian=${UseJacobian}
+       --usejacobian=${UseJacobian} \
+       --boldmask=${BOLDMask}
 
 #Copy selected files to ResultsFolder
 ${RUN} cp ${fMRIFolder}/${NameOffMRI}_nonlin_norm.nii.gz ${ResultsFolder}/${NameOffMRI}.nii.gz

fMRIVolume/scripts/IntensityNormalization.sh

@@ -1,5 +1,6 @@
-#!/bin/bash 
+#!/bin/bash
 set -e
+source ${HCPPIPEDIR}/global/scripts/debug.shlib # Debugging functions
 
 # Intensity normalisation, and bias field correction, and optional Jacobian modulation, applied to fMRI images (all inputs must be in fMRI space)
 
@@ -35,18 +36,23 @@ Usage() {
   echo "             [--inscout=<input name for scout image (pre-sat EPI)>]"
   echo "             [--oscout=<output name for normalized scout image>]"
   echo "             [--workingdir=<working dir>]"
+  echo "             [--boldmask=<what mask to use for generating final BOLD timeseries:"
+  echo "                         T1_fMRI_FOV (default): mask based on T1 and voxels available at all timepoints (i.e., the fMRI FOV)"
+  echo "                         T1_DILATED_fMRI_FOV: a once dilated T1w brain based mask combined with fMRI FOV"
+  echo "                         T1_DILATED2x_fMRI_FOV: a twice dilated T1w brain based mask combined with fMRI FOV,"
+  echo "                         fMRI_FOV: a fMRI FOV mask"
 }
 
 # function for parsing options
 getopt1() {
     sopt="$1"
     shift 1
     for fn in $@ ; do
-	if [ `echo $fn | grep -- "^${sopt}=" | wc -w` -gt 0 ] ; then
-	    echo $fn | sed "s/^${sopt}=//"
-	    # if [ ] ; then Usage ; echo " " ; echo "Error:: option ${sopt} requires an argument"; exit 1 ; end
-	    return 0
-	fi
+  if [ `echo $fn | grep -- "^${sopt}=" | wc -w` -gt 0 ] ; then
+      echo $fn | sed "s/^${sopt}=//"
+      # if [ ] ; then Usage ; echo " " ; echo "Error:: option ${sopt} requires an argument"; exit 1 ; end
+      return 0
+  fi
     done
 }
 
@@ -75,10 +81,27 @@ OutputfMRI=`getopt1 "--ofmri" $@`  # "$5"
 ScoutInput=`getopt1 "--inscout" $@`  # "$6"
 ScoutOutput=`getopt1 "--oscout" $@`  # "$7"
 UseJacobian=`getopt1 "--usejacobian" $@`  # 
+BOLDMask=`getopt1 "--boldmask" $@`
+
+verbose_red_echo "---> Intensity normalization"
+
+verbose_echo " "
+verbose_echo " Using parameters ..."
+verbose_echo "          --infmri: ${InputfMRI}"
+verbose_echo "       --biasfield: ${BiasField}"
+verbose_echo "        --jacobian: ${Jacobian}"
+verbose_echo "       --brainmask: ${BrainMask}"
+verbose_echo "           --ofmri: ${OutputfMRI}"
+verbose_echo "         --inscout: ${ScoutInput}"
+verbose_echo "          --oscout: ${ScoutOutput}"
+verbose_echo "     --usejacobian: ${UseJacobian}"
+verbose_echo "         --boldmask: ${BOLDMask}"
+verbose_echo " "
 
 # default parameters
 OutputfMRI=`$FSLDIR/bin/remove_ext $OutputfMRI`
 WD=`defaultopt $WD ${OutputfMRI}.wdir`
+BOLDMask=`defaultopt $BOLDMask "T1_fMRI_FOV"`
 
 #sanity check the jacobian option
 if [[ "$UseJacobian" != "true" && "$UseJacobian" != "false" ]]
@@ -89,7 +112,7 @@ fi
 
 jacobiancom=""
 if [[ $UseJacobian == "true" ]] ; then
-  jacobiancom="-mul $Jacobian"
+    jacobiancom="-mul $Jacobian"
 fi
 
 biascom=""
@@ -99,10 +122,10 @@ then
 fi
 
 # sanity checking
-if [ X${ScoutInput} != X ] ; then 
+if [ X${ScoutInput} != X ] ; then
     if [ X${ScoutOutput} = X ] ; then
-    	echo "Error: Must supply an output name for the normalised scout image"
-    	exit 1
+      echo "Error: Must supply an output name for the normalised scout image"
+      exit 1
     fi
 fi
 
@@ -117,20 +140,49 @@ echo "PWD = `pwd`" >> $WD/log.txt
 echo "date: `date`" >> $WD/log.txt
 echo " " >> $WD/log.txt
 
+########################################## DO WORK ##########################################
 
-########################################## DO WORK ########################################## 
-
-# FinalMask is a combination of the FS-derived brainmask, and the spatial coverage mask that captures the
-# voxels that have data available at *ALL* time points (derived in OneStepResampling)
 FinalMask=`${FSLDIR}/bin/remove_ext ${InputfMRI}`_finalmask
-${FSLDIR}/bin/fslmaths ${BrainMask} -bin -mas ${InputfMRI}_mask ${FinalMask}
+T1FOVMask=`${FSLDIR}/bin/remove_ext ${InputfMRI}`_T1FOVmask
+${FSLDIR}/bin/fslmaths ${BrainMask} -bin -mas ${InputfMRI}_mask ${T1FOVMask}
+
+# Use the requested BOLD mask 
+
+if [ "${BOLDMask}" = "T1_fMRI_FOV" ] ; then
+    # FinalMask is a combination of the FS-derived brainmask, and the spatial coverage mask that captures the
+    # voxels that have data available at *ALL* time points (derived in OneStepResampling)
+    ${FSLDIR}/bin/imcp ${T1FOVMask} ${FinalMask}
+
+elif [ "${BOLDMask}" = "T1_DILATED_fMRI_FOV" ] ; then
+    # FinalMask is a combination of once dilated FS-derived brainmask, and the spatial coverage mask that captures the
+    # voxels that have data available at *ALL* time points (derived in OneStepResampling)
+    ${FSLDIR}/bin/fslmaths ${BrainMask} -bin -dilF -mas ${InputfMRI}_mask ${FinalMask}
+
+elif [ "${BOLDMask}" = "T1_DILATED2x_fMRI_FOV" ] ; then
+    # FinalMask is a combination of twice dilated FS-derived brainmask, and the spatial coverage mask that captures the
+    # voxels that have data available at *ALL* time points (derived in OneStepResampling)
+    ${FSLDIR}/bin/fslmaths ${BrainMask} -bin -dilF -dilF -mas ${InputfMRI}_mask ${FinalMask}
+
+elif [ "${BOLDMask}" = "fMRI_FOV" ] ; then
+    # FinalMask is the spatial coverage mask that captures the
+    # voxels that have data available at *ALL* time points (derived in OneStepResampling)
+    ${FSLDIR}/bin/imcp ${InputfMRI}_mask ${FinalMask}
+
+elif
+    # No valid BOLDMask option was specified
+    log_Err_Abort "Invalid entry for specified BOLD mask (--boldmask=${BOLDMask})"
+fi
 
-# Create a simple summary text file of the percentage of spatial coverage of the fMRI data inside the FS-derived brain mask
+
+# Create a simple summary text file of the percentage of spatial coverage of the fMRI data inside the FS-derived brain mask and the actual mask used
 NvoxBrainMask=`fslstats ${BrainMask} -V | awk '{print $1}'`
+NvoxT1FOVMask=`fslstats ${T1FOVMask} -V | awk '{print $1}'`
 NvoxFinalMask=`fslstats ${FinalMask} -V | awk '{print $1}'`
-PctCoverage=`echo "scale=4; 100 * ${NvoxFinalMask} / ${NvoxBrainMask}" | bc -l`
-echo "PctCoverage, NvoxFinalMask, NvoxBrainMask" >| ${FinalMask}.stats.txt
-echo "${PctCoverage}, ${NvoxFinalMask}, ${NvoxBrainMask}" >> ${FinalMask}.stats.txt
+PctBrainCoverage=`echo "scale=4; 100 * ${NvoxT1FOVMask} / ${NvoxBrainMask}" | bc -l`
+PctMaskCoverage=`echo "scale=4; 100 * ${NvoxFinalMask} / ${NvoxT1FOVMask}" | bc -l`
+echo "BOLDMask, PctBrainCoverage, PctMaskCoverage, NvoxT1FOVMask, NvoxBrainMask, NvoxFinalMask" >| ${FinalMask}.stats.txt
+echo "${BOLDMask}, ${PctBrainCoverage}, ${PctMaskCoverage}, ${NvoxT1FOVMask}, ${NvoxBrainMask}, ${NvoxFinalMask}" >> ${FinalMask}.stats.txt
+
 
 # Run intensity normalisation, with bias field correction and optional jacobian modulation,
 # for the main fmri timeseries and the scout images (pre-saturation images)
@@ -146,7 +198,7 @@ echo " "
 echo "END: IntensityNormalization"
 echo " END: `date`" >> $WD/log.txt
 
-########################################## QA STUFF ########################################## 
+########################################## QA STUFF ##########################################
 
 if [ -e $WD/qa.txt ] ; then rm -f $WD/qa.txt ; fi
 echo "cd `pwd`" >> $WD/qa.txt