Merge pull request #7 from madisoth/master

10.5T branch commits + new pipeline options
DCAN-Labs · Aug 4, 2021 · df17842 · df17842
2 parents e31ab3a + c9a7967
commit df17842
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Showing 11 changed files with 948 additions and 277 deletions.
diff --git a/Examples/Scripts/PreFreeSurferPipeLine.bat b/Examples/Scripts/PreFreeSurferPipeLine.bat
@@ -84,6 +84,8 @@ for Subject in $Subjlist ; do
   T2wTemplate2mm="${HCPPIPEDIR_Templates}/MacaqueYerkes19_T2w_1.0mm_grad.nii.gz" #MacaqueYerkes1.0mm T2wTemplate
   TemplateMask="${HCPPIPEDIR_Templates}/MacaqueYerkes19_T1w_0.5mm_brain_mask_dil.nii.gz" #Brain mask MacaqueYerkes0.5mm template
   Template2mmMask="${HCPPIPEDIR_Templates}/MacaqueYerkes19_T1w_1.0mm_brain_mask_dil.nii.gz" #MacaqueYerkes1.0mm template
+  StudyTemplate="${HCPPIPEDIR_Templates}/MacaqueYerkes19_T1w_0.5mm_grad.nii.gz"
+  StudyTemplateBrain="${HCPPIPEDIR_Templates}/MacaqueYerkes19_T1w_0.5mm_brain.nii.gz"
 
   #Scan Settings
   TE="2.46" #delta TE in ms for field map or "NONE" if not used
@@ -100,6 +102,7 @@ for Subject in $Subjlist ; do
   AvgrdcSTRING="FIELDMAP" #Averaging and readout distortion correction methods: "NONE" = average any repeats with no readout correction "FIELDMAP" = average any repeats and use field map for readout correction "TOPUP" = Use Spin Echo FieldMap
   TopupConfig="NONE" #Config for topup or "NONE" if not used
   BiasFieldSmoothingSigma="1.5"
+  useAntsReg="false"
 
   ${FSLDIR}/bin/fsl_sub ${QUEUE} \
      ${HCPPIPEDIR}/PreFreeSurfer/PreFreeSurferPipeline.sh \
@@ -131,6 +134,9 @@ for Subject in $Subjlist ; do
       --avgrdcmethod="$AvgrdcSTRING" \
       --topupconfig="$TopupConfig" \
       --bfsigma="$BiasFieldSmoothingSigma" \
+      --useAntsReg="${useAntsReg}" \
+      --StudyTemplate="${StudyTemplate}" \
+      --StudyTemplateBrain="${StudyTemplateBrain}" \
       --printcom=$PRINTCOM
 
   # The following lines are used for interactive debugging to set the positional parameters: $1 $2 $3 ...
@@ -163,6 +169,9 @@ for Subject in $Subjlist ; do
       --avgrdcmethod=${AvgrdcSTRING} \
       --topupconfig=${TopupConfig} \
       --bfsigma=${BiasFieldSmoothingSigma} \
+      --useAntsReg=${useAntsReg} \
+      --StudyTemplate=${StudyTemplate} \
+      --StudyTemplateBrain=${StudyTemplateBrain} \
       --printcom=${PRINTCOM}"
 
   echo ". ${EnvironmentScript}"

diff --git a/Examples/Scripts/PreFreeSurferPipelineBatch.sh b/Examples/Scripts/PreFreeSurferPipelineBatch.sh
@@ -469,7 +469,7 @@ main()
 			--brainsize="$BrainSize" \
 			--fnirtconfig="$FNIRTConfig" \
 			--fmapmag="$MagnitudeInputName" \
-                        --fmapmagbrain="$StudyFolder"/masks/$(basename $(remove_ext "$MagnitudeInputName"))_brain.nii.gz \
+			--fmapmagbrain="$StudyFolder"/masks/$(basename $(remove_ext "$MagnitudeInputName"))_brain.nii.gz \
 			--fmapphase="$PhaseInputName" \
 			--fmapgeneralelectric="$GEB0InputName" \
 			--echodiff="$TE" \
@@ -482,8 +482,8 @@ main()
 			--unwarpdir="$UnwarpDir" \
 			--gdcoeffs="$GradientDistortionCoeffs" \
 			--avgrdcmethod="$AvgrdcSTRING" \
-			--topupconfig="$TopupConfig" \
-                        --useT2="$useT2" \
+            --topupconfig="$TopupConfig" \
+			--useT2="$useT2" \
 			--t1normalized="$T1wNormalized" \
 			--printcom=$PRINTCOM \
 			--revepi=${ReverseEpi:-false}

diff --git a/FreeSurfer/FreeGreyPipeline.sh b/FreeSurfer/FreeGreyPipeline.sh
@@ -31,6 +31,20 @@ useT2=`opts_GetOpt1 "--useT2" $@` #AP 20162111
 MaxThickness=`opts_GetOpt1 "--maxThickness" $@` # Max threshold for thickness measurements (default = 5mm)
 NormMethod=`opts_GetOpt1 "--normalizationMethod" $@` # Normalization method to be used (or none)
 hypernormalize=`opts_GetOpt1 "--hypernormalize" $@` #deprecated - lose after BIDSApp doesn't use it anymore.
+NormGMStdDevScale=`opts_GetOpt1 "--normgmstddevscale" $@` # normalized GM std dev scale factor
+NormWMStdDevScale=`opts_GetOpt1 "--normwmstddevscale" $@` # normalized WM std dev scale factor
+NormCSFStdDevScale=`opts_GetOpt1 "--normcsfstddevscale" $@` # normalized CSF std dev scale factor
+
+# option to make white surface from adult-normalized T1w (if it exists)
+MakeWhiteFromNormT1=`opts_GetOpt1 "--makewhitefromnormt1" $@`
+MakeWhiteFromNormT1="$(echo ${MakeWhiteFromNormT1} | tr '[:upper:]' '[:lower:]')" # to lower case
+
+# option to keep the pial surface generated from initial pass of mris_make_surfaces 
+# (using the hypernormalized brain.AN.mgz T1w image, unless hypernormalization was omitted)
+# instead of using it as a prior for a 2nd pass of mris_make_surfaces
+# (2nd pass uses the non-hypernormalized brain.finalsurfs.mgz T1w by default)
+SinglePassPial=`opts_GetOpt1 "--singlepasspial" $@` 
+SinglePassPial="$(echo ${SinglePassPial} | tr '[:upper:]' '[:lower:]')" # to lower case
 
 if [ -z "${NormMethod}" ] ; then
     # Default is to use the adult grey matter intensity profile.
@@ -59,7 +73,7 @@ Subnum=$SubjectID
 if [[ "${NormMethod^^}" == "NONE" ]] ; then
     echo Skipping hyper-normalization step per request.
 else
-    ${HCPPIPEDIR_FS}/hypernormalize.sh ${SubjectDIR} ${NormMethod^^}
+    ${HCPPIPEDIR_FS}/hypernormalize.sh ${SubjectDIR} ${NormMethod^^} ${NormGMStdDevScale} ${NormWMStdDevScale} ${NormCSFStdDevScale}
     T1wNImage="T1wN_acpc.nii.gz"
     T1wNImageBrain="T1wN_acpc_brain.nii.gz"
     echo T1wNImage=$T1wNImage
@@ -274,6 +288,7 @@ for TXw in $Modalities; do
   popd
 done
 SubjectID=$Subnum
+
 #grab white matter
 fslmaths ${AsegFile}_1mm.nii.gz -thr 41 -uthr 41 -bin blah41.nii.gz
 fslmaths ${AsegFile}_1mm.nii.gz -thr 2 -uthr 2 -bin blah2.nii.gz
@@ -287,7 +302,23 @@ mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
 mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz wm.mgz filled.mgz
 popd
 echo "BEGIN: recon-all"
-recon-all -subjid ${SubjectID} -tessellate -smooth1 -inflate1 -qsphere -fix -white -smooth2 -inflate2 -sphere
+
+recon-all -subjid ${SubjectID} -tessellate -smooth1 -inflate1 -qsphere -fix
+
+if [ $MakeWhiteFromNormT1 = true ] && [ ! -z $T1wNImage ]; then
+  # make white surfaces from adult-normalized T1w
+  echo "Making white surfaces from normalized T1w"
+  # copy adult-normalized T1w volume to main subject mri dir 
+  cp -T -n ${SubjectID}N/mri/brain.finalsurfs.mgz ${SubjectID}/mri/brain.AN.mgz
+  for hemi in l r; do
+    mris_make_surfaces -whiteonly -noaparc -mgz -T1 brain.AN ${SubjectID} ${hemi}h
+else
+    # make white surfaces from non-normalized T1w (same as default recon-all -white)
+  for hemi in l r; do
+    mris_make_surfaces -whiteonly -noaparc -mgz -T1 brain.finalsurfs ${SubjectID} ${hemi}h
+fi
+
+recon-all -subjid ${SubjectID} -smooth2 -inflate2 -sphere
 # Using monkey .tif for calculating surface registration.
 echo "Registering surface using average.curvature.filled from MacaqueYerkes19"
 pushd ${SUBJECTS_DIR}/${SubjectID}/surf
@@ -308,13 +339,25 @@ if [ ! -z $T1wNImage ]; then
     cp -T -n ${SubjectID}/surf/"${hemi}"h.pial ${SubjectID}/surf/"${hemi}"h.pial.noAN
     #mris_make_surfaces ${MAXTHICKNESS} -orig_white white.noAN -white NOWRITE -mgz -T1 brain.AN $SubjectID ${hemi}h
     mris_make_surfaces ${MAXTHICKNESS} -white NOWRITE -mgz -T1 brain.AN $SubjectID ${hemi}h
-    mris_make_surfaces ${MAXTHICKNESS} -orig_pial pial -white NOWRITE -mgz -T1 brain.finalsurfs $SubjectID ${hemi}h
+      # if true, skip 2nd pass of mris_make_surfaces
+      # and keep the pial derived from adult-normalized brain as the final surface
+    if [ $SinglePassPial = false ]; then 
+      mris_make_surfaces ${MAXTHICKNESS} -orig_pial pial -white NOWRITE -mgz -T1 brain.finalsurfs $SubjectID ${hemi}h
+    else
+      echo "Using single pass pial"
+    fi
   done
 else
   for hemi in l r; do
     #mris_make_surfaces ${MAXTHICKNESS} -orig_white white.noAN -white NOWRITE -mgz -T1 brain.AN $SubjectID ${hemi}h
     mris_make_surfaces ${MAXTHICKNESS} -white NOWRITE -mgz -T1 brain.finalsurfs $SubjectID ${hemi}h
-    mris_make_surfaces ${MAXTHICKNESS} -orig_pial pial -white NOWRITE -mgz -T1 brain.finalsurfs $SubjectID ${hemi}h
+      # if true, skip 2nd pass of mris_make_surfaces
+      # and keep the initial pial as the final surface
+    if [ $SinglePassPial = false ]; then
+      mris_make_surfaces ${MAXTHICKNESS} -orig_pial pial -white NOWRITE -mgz -T1 brain.finalsurfs $SubjectID ${hemi}h
+    else
+      echo "Using single pass pial"
+    fi
   done
 fi
 

diff --git a/FreeSurfer/scripts/Change2AdultIntensity.bash b/FreeSurfer/scripts/Change2AdultIntensity.bash
@@ -8,9 +8,18 @@ base_image=$1
 adult_image=$2 #adult freesurfer atlas
 # EXAMPLE means_RB_all
 
+NormGMStdDevScale=$3 # scaling factor for standard deviation of the normalized gray matter (relative to the standard deviation of the reference adult GM image).
+# If T1w_acpc_dc_restore has regions of low/uneven GM intensity causing issues with surface generation,
+# reducing SD (e.g. scaling by 0.5) may yield improvement. 
+# Alternatively, consider manually setting these threshold values used by FreeSurfer's mris_make_surfaces:
+# MIN_GRAY_AT_WHITE_BORDER, MAX_GRAY, MAX_GRAY_AT_CSF_BORDER, MIN_GRAY_AT_CSF_BORDER 
+
+
+NormWMStdDevScale=$4 # scaling factor for standard deviation of the normalized white matter (relative to the standard deviation of the reference adult WM image.)
+
 #Changing intensities of monkey WM,GM and CSF to match adult freesurfer template
-fslmaths ${base_image} -sub `fslstats ${base_image}_GM -M` -div `fslstats ${base_image}_GM -S` -mul `fslstats ${adult_image}_GM -S` -add `fslstats ${adult_image}_GM -M` ${base_image}_GMshifted
-fslmaths ${base_image} -sub `fslstats ${base_image}_WM -M` -div `fslstats ${base_image}_WM -S` -mul `fslstats ${adult_image}_WM -S` -add `fslstats ${adult_image}_WM -M` -mas ${base_image}_WM  ${base_image}_WM_AdultInt
+fslmaths ${base_image} -sub `fslstats ${base_image}_GM -M` -div `fslstats ${base_image}_GM -S` -mul `fslstats ${adult_image}_GM -S` -mul ${NormGMStdDevScale} -add `fslstats ${adult_image}_GM -M` ${base_image}_GMshifted
+fslmaths ${base_image} -sub `fslstats ${base_image}_WM -M` -div `fslstats ${base_image}_WM -S` -mul `fslstats ${adult_image}_WM -S` -mul ${NormWMStdDevScale} -add `fslstats ${adult_image}_WM -M` -mas ${base_image}_WM  ${base_image}_WM_AdultInt
 
 #Replace WM in GM_shifted with shifted WM
 

diff --git a/FreeSurfer/scripts/ChangeROIs2AdultIntensity.bash b/FreeSurfer/scripts/ChangeROIs2AdultIntensity.bash
@@ -6,10 +6,20 @@
 base_image=$1   # EXAMPLE T1w_acpc_dc_restore - do not include file extensions
 adult_image=$2  # THIS IS ADULT FREESURFER ATLAS-GET INTENSITIES FROM HERE; EXAMPLE means_RB_all
 
+NormGMStdDevScale=$3 # scaling factor for standard deviation of the normalized gray matter (relative to the standard deviation of the reference adult GM image).
+# If T1w_acpc_dc_restore has regions of low/uneven GM intensity causing issues with surface generation,
+# reducing SD (e.g. scaling by 0.5) may help. 
+# Alternatively, consider manually setting these threshold values used by FreeSurfer's mris_make_surfaces:
+# MIN_GRAY_AT_WHITE_BORDER, MAX_GRAY, MAX_GRAY_AT_CSF_BORDER, MIN_GRAY_AT_CSF_BORDER 
+
+NormWMStdDevScale=$4 # scaling factor for standard deviation of the normalized white matter (relative to the standard deviation of the reference adult WM image).
+
+NormCSFStdDevScale=$5 # scaling factor for standard deviation of the normalized CSF (relative to the standard deviation of the reference adult CSF image).
+
 # Change intensities of monkey WM,GM and CSF to match adult freesurfer template.
-fslmaths ${base_image}_WM -sub `fslstats ${base_image}_WM -M` -div `fslstats ${base_image}_WM -S` -mul `fslstats ${adult_image}_WM -S` -add `fslstats ${adult_image}_WM -M` -mas ${base_image}_WM  ${base_image}_WM_AdultInt
-fslmaths ${base_image}_GM -sub `fslstats ${base_image}_GM -M` -div `fslstats ${base_image}_GM -S` -mul `fslstats ${adult_image}_GM -S` -add `fslstats ${adult_image}_GM -M` -mas ${base_image}_GM  ${base_image}_GM_AdultInt
-fslmaths ${base_image}_CSF -sub `fslstats ${base_image}_CSF -M` -div `fslstats ${base_image}_CSF -S` -mul `fslstats ${adult_image}_CSF -S` -add `fslstats ${adult_image}_CSF -M` -mas ${base_image}_CSF  ${base_image}_CSF_AdultInt
+fslmaths ${base_image}_WM -sub `fslstats ${base_image}_WM -M` -div `fslstats ${base_image}_WM -S` -mul `fslstats ${adult_image}_WM -S` -mul ${NormGMStdDevScale} -add `fslstats ${adult_image}_WM -M` -mas ${base_image}_WM  ${base_image}_WM_AdultInt
+fslmaths ${base_image}_GM -sub `fslstats ${base_image}_GM -M` -div `fslstats ${base_image}_GM -S` -mul `fslstats ${adult_image}_GM -S` -mul ${NormWMStdDevScale} -add `fslstats ${adult_image}_GM -M` -mas ${base_image}_GM  ${base_image}_GM_AdultInt
+fslmaths ${base_image}_CSF -sub `fslstats ${base_image}_CSF -M` -div `fslstats ${base_image}_CSF -S` -mul `fslstats ${adult_image}_CSF -S` -mul ${NormCSFStdDevScale} -add `fslstats ${adult_image}_CSF -M` -mas ${base_image}_CSF  ${base_image}_CSF_AdultInt
 
 # Put monkey image back together.
 fslmaths ${base_image}_WM_AdultInt -add ${base_image}_GM_AdultInt -add ${base_image}_CSF_AdultInt ${base_image}_AdultInt

diff --git a/FreeSurfer/scripts/hypernormalize.sh b/FreeSurfer/scripts/hypernormalize.sh
@@ -10,6 +10,9 @@ echo SOURCE_DIR=${SOURCE_DIR}
 
 subjectdir=$1
 NormMethod=$2
+NormGMStdDevScale=$3
+NormWMStdDevScale=$4
+NormCSFStdDevScale=$5
 if [ -z  "${NormMethod}" ] ; then
     # Default is to use the adult grey matter intensity profile.
     NormMethod="ADULT_GM_IP"
@@ -21,10 +24,10 @@ ${SOURCE_DIR}/make_WMGMCSF_masks.sh T1w_acpc_dc_restore.nii.gz aseg_acpc.nii.gz
 
 if [[ "${NormMethod^^}" == "ROI_IPS" ]] ; then
     # Call the old script that changes each ROI's intensity profile and puts them back together.
-    ${SOURCE_DIR}/ChangeROIs2AdultIntensity.bash T1w_acpc_dc_restore ${HCPPIPEDIR_Templates}/means_RB_all
+    ${SOURCE_DIR}/ChangeROIs2AdultIntensity.bash T1w_acpc_dc_restore ${HCPPIPEDIR_Templates}/means_RB_all ${NormGMStdDevScale} ${NormWMStdDevScale} ${NormCSFStdDevScale}
 else
     # Default: call script to change whole brain based on grey matter in adult ref.
-    ${SOURCE_DIR}/Change2AdultIntensity.bash T1w_acpc_dc_restore ${HCPPIPEDIR_Templates}/means_RB_all
+    ${SOURCE_DIR}/Change2AdultIntensity.bash T1w_acpc_dc_restore ${HCPPIPEDIR_Templates}/means_RB_all ${NormGMStdDevScale} ${NormWMStdDevScale} 
 fi
 mv T1w_acpc_dc_restore_AdultInt_thr.nii.gz T1wN_acpc.nii.gz
 ${FSLDIR}/bin/fslmaths T1wN_acpc.nii.gz -mas T1w_acpc_dc_restore_brain.nii.gz T1wN_acpc_brain.nii.gz