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FreeSurfer2HCPWorkbenchConverter.sh
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#!/bin/bash
set -e
#set -x
# Requirements for this script
# installed versions of: FSL (version 5.0.6), FreeSurfer (version 5.3.0-HCP), wb_command
# environment: FSLDIR , FREESURFER_HOME , HCPPIPEDIR , CARET7DIR
# Author: Alex Cohen, adapted from HCP Pipelines code, cloned at commit b8ea1db
# --------------------------------------------------------------------------------
# Load Function Libraries
# --------------------------------------------------------------------------------
source $HCPPIPEDIR/global/scripts/log.shlib # Logging related functions
source $HCPPIPEDIR/global/scripts/opts.shlib # Command line option functions
########################################## SUPPORT FUNCTIONS ##########################################
# --------------------------------------------------------------------------------
# Usage Description Function
# --------------------------------------------------------------------------------
show_usage() {
echo "This makes a subdir /hcp and creates wb_view .spec files from the FS output"
echo " Inputs:"
echo " --subject=fc_12345"
echo " [--path=/blah/blah/blah] if not specified, assumes pwd"
echo " [[email protected]] to make more cortical surfaces (0->1 ~ white->pial)"
echo " [--subcort=1.3@2] to make subcortical surfaces (mm below white)"
echo " [--target=rawavg] if not specified, assumes T1"
echo " [--lowres=8] 8=8,412nodes, 32=32,492 nodes. Will always make 32k, specify if other resolutions desired"
exit 1
}
defaultopt() {
echo $1
}
# --------------------------------------------------------------------------------
# Establish tool name for logging
# --------------------------------------------------------------------------------
log_SetToolName "FreeSurfer2HCPWorkbenchConverter.sh"
################################################## OPTION PARSING #####################################################
opts_ShowVersionIfRequested $@
if opts_CheckForHelpRequest $@; then
show_usage
fi
if [ $# -eq 0 ] ; then
show_usage
fi
log_Msg "Parsing Command Line Options"
# Input Variables
StudyFolder=`opts_GetOpt1 "--path" $@`
Subject=`opts_GetOpt1 "--subject" $@`
Layers=`opts_GetOpt1 "--layers" $@`
Subcort=`opts_GetOpt1 "--subcort" $@`
Target=`opts_GetOpt1 "--target" $@`
LowResMesh=`opts_GetOpt1 "--lowres" $@`
#Initializing Variables with Default Values if not otherwise specified
WD=`pwd`
StudyFolder=`defaultopt $StudyFolder $WD`
Layers=`defaultopt $Layers ""`
Subcort=`defaultopt $Subcort ""`
Target=`defaultopt $Target T1`
LowResMeshes=`echo $LowResMesh "32"`
FreeSurferFolder="$StudyFolder"/"$Subject"
SUBJECTS_DIR="$StudyFolder"
# Hardcoded parameters
HCPFolder="$FreeSurferFolder"/hcp
FreeSurferLabels="${HCPPIPEDIR_Config}/FreeSurferAllLut.txt"
SurfaceAtlasDIR="${HCPPIPEDIR_Templates}/standard_mesh_atlases"
HighResMesh="164"
RegName="FS"
GrayordinatesSpaceDIR="${HCPPIPEDIR_Templates}/91282_Greyordinates"
# Make output folder
if [ ! -e "$HCPFolder" ] ; then
mkdir -p "$HCPFolder"
else
echo "*******"
echo "WARNING: The hcp sub-directory already exists, are you sure you want to re-run this script?"
echo "*******"
read -p "(y or n): " -n 1 -r REPLY
echo ""
if [[ ! $REPLY =~ ^[Yy]$ ]]
then
exit 1
fi
fi
#Find c_ras offset between FreeSurfer surface and volume and generate matrix to transform surfaces
MatrixX=`mri_info "$FreeSurferFolder"/mri/brain.finalsurfs.mgz | grep "c_r" | cut -d "=" -f 5 | sed s/" "/""/g`
MatrixY=`mri_info "$FreeSurferFolder"/mri/brain.finalsurfs.mgz | grep "c_a" | cut -d "=" -f 5 | sed s/" "/""/g`
MatrixZ=`mri_info "$FreeSurferFolder"/mri/brain.finalsurfs.mgz | grep "c_s" | cut -d "=" -f 5 | sed s/" "/""/g`
echo "1 0 0 ""$MatrixX" > "$FreeSurferFolder"/mri/c_ras.mat
echo "0 1 0 ""$MatrixY" >> "$FreeSurferFolder"/mri/c_ras.mat
echo "0 0 1 ""$MatrixZ" >> "$FreeSurferFolder"/mri/c_ras.mat
echo "0 0 0 1" >> "$FreeSurferFolder"/mri/c_ras.mat
#Convert FreeSurfer Volumes (and transform to $Target, if not T1.mgz)
for Image in wmparc aparc.a2009s+aseg aparc+aseg ; do
if [ -e "$FreeSurferFolder"/mri/"$Image".mgz ] ; then
if [ ! $Target = "T1" ] ; then
mri_label2vol --seg "$FreeSurferFolder"/mri/"$Image".mgz --temp "$FreeSurferFolder"/mri/"$Target".mgz --o "$FreeSurferFolder"/mri/"$Image"-in-"$Target".mgz --regheader "$FreeSurferFolder"/mri/"$Image".mgz
NewImage=`echo ${Image}-in-"${Target}"`
touch "$HCPFolder"/All_Files_are_registered_to_"$Target"
else
NewImage=$Image
touch "$HCPFolder"/All_Files_are_registered_to_T1
fi
mri_convert -ot nii "$FreeSurferFolder"/mri/"$NewImage".mgz "$HCPFolder"/"$Image".nii.gz
fslreorient2std "$HCPFolder"/"$Image".nii.gz "$HCPFolder"/"$Image".nii.gz
${CARET7DIR}/wb_command -volume-label-import "$HCPFolder"/"$Image".nii.gz "$FreeSurferLabels" "$HCPFolder"/"$Image".nii.gz -drop-unused-labels
fi
done
#Add Anatomical Volumes
for Image in $Target ; do
if [ -e "$FreeSurferFolder"/mri/"$Image".mgz ] ; then
mri_convert -ot nii "$FreeSurferFolder"/mri/"$Image".mgz "$HCPFolder"/"$Image".nii.gz
fslreorient2std "$HCPFolder"/"$Image".nii.gz "$HCPFolder"/"$Image".nii.gz
pushd > /dev/null "$HCPFolder"
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject".native.wb.spec INVALID ./"$Image".nii.gz
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec INVALID ./"$Image".nii.gz
popd > /dev/null
fi
done
#Loop through left and right hemispheres
for Hemisphere in L R ; do
#Set a bunch of different ways of saying left and right
if [ $Hemisphere = "L" ] ; then
hemisphere="l"
Structure="CORTEX_LEFT"
elif [ $Hemisphere = "R" ] ; then
hemisphere="r"
Structure="CORTEX_RIGHT"
fi
#native Mesh Processing
#Convert and volumetrically register white and pial surfaces makign linear and nonlinear copies, add each to the appropriate spec file
Types="ANATOMICAL@GRAY_WHITE ANATOMICAL@PIAL"
i=1
for Surface in white pial ; do
Type=`echo "$Types" | cut -d " " -f $i`
Secondary=`echo "$Type" | cut -d "@" -f 2`
Type=`echo "$Type" | cut -d "@" -f 1`
if [ ! $Secondary = $Type ] ; then
Secondary=`echo " -surface-secondary-type ""$Secondary"`
else
Secondary=""
fi
if [ ! $Target = "T1" ] ; then
tkregister2 --mov "$FreeSurferFolder"/mri/"$Target".mgz --targ "$FreeSurferFolder"/mri/orig.mgz --reg "$FreeSurferFolder"/mri/register."$Target".dat --noedit --regheader
mri_surf2surf --sval-xyz "$Surface" --reg "$FreeSurferFolder"/mri/register."$Target".dat "$FreeSurferFolder"/mri/"$Target".mgz --tval "$hemisphere"h."$Surface"."$Target" --tval-xyz --hemi "$hemisphere"h --s $Subject
NewSurface=`echo ${Surface}.${Target}`
else
NewSurface=$Surface
fi
mris_convert "$FreeSurferFolder"/surf/"$hemisphere"h."$NewSurface" "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
${CARET7DIR}/wb_command -set-structure "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${Structure} -surface-type $Type$Secondary
${CARET7DIR}/wb_command -surface-apply-affine "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii "$FreeSurferFolder"/mri/c_ras.mat "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
pushd > /dev/null "$HCPFolder"
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject".native.wb.spec $Structure ./"$Subject"."$Hemisphere"."$Surface".native.surf.gii
popd > /dev/null
i=$(($i+1))
done
#Create midthickness by averaging white and pial surfaces and use it to make inflated surfacess
for Folder in "$HCPFolder" ; do
pushd > /dev/null "$Folder"
${CARET7DIR}/wb_command -surface-average "$Folder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii -surf "$Folder"/"$Subject"."$Hemisphere".white.native.surf.gii -surf "$Folder"/"$Subject"."$Hemisphere".pial.native.surf.gii
${CARET7DIR}/wb_command -set-structure "$Folder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii ${Structure} -surface-type ANATOMICAL -surface-secondary-type MIDTHICKNESS
${CARET7DIR}/wb_command -add-to-spec-file "$Folder"/"$Subject".native.wb.spec $Structure ./"$Subject"."$Hemisphere".midthickness.native.surf.gii
${CARET7DIR}/wb_command -surface-generate-inflated "$Folder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$Folder"/"$Subject"."$Hemisphere".inflated.native.surf.gii "$Folder"/"$Subject"."$Hemisphere".very_inflated.native.surf.gii -iterations-scale 2.5
${CARET7DIR}/wb_command -add-to-spec-file "$Folder"/"$Subject".native.wb.spec $Structure ./"$Subject"."$Hemisphere".inflated.native.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$Folder"/"$Subject".native.wb.spec $Structure ./"$Subject"."$Hemisphere".very_inflated.native.surf.gii
#Create subcortical surface by eroding the white surface
if [ -z "$Subcort" ] ; then
echo "Not creating subcortical surfaces"
else
echo "Creating subcortical surfaces"
SubcortList=`echo ${Subcort} | sed 's/@/ /g'`
SubcortNameList=`echo subcortlayer_mm_${Subcort} | sed 's/@/ subcortlayer_mm_/g'`
for EachSubLayer in $SubcortList; do
if [ ! $Target = "T1" ] ; then
TargetSuffix=."$Target"
else
TargetSuffix=""
fi
mris_expand "$FreeSurferFolder"/surf/"$hemisphere"h.white"$TargetSuffix" -${EachSubLayer} "$FreeSurferFolder"/surf/"$hemisphere"h.subcortlayer_mm_"$EachSubLayer""$TargetSuffix"
done
for Surface in $SubcortNameList ; do
if [ ! $Target = "T1" ] ; then
NewSurface=`echo ${Surface}.${Target}`
else
NewSurface=$Surface
fi
mris_convert "$FreeSurferFolder"/surf/"$hemisphere"h."$NewSurface" "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
${CARET7DIR}/wb_command -set-structure "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${Structure} -surface-type ANATOMICAL -surface-secondary-type INVALID
${CARET7DIR}/wb_command -surface-apply-affine "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii "$FreeSurferFolder"/mri/c_ras.mat "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject".native.wb.spec $Structure ./"$Subject"."$Hemisphere"."$Surface".native.surf.gii
done
fi
#Create ADDITIONAL cortical layers by averaging white and pial surfaces with variable distance from the surfaces
if [ -z "$Layers" ] ; then
echo "Not creating additional cortical layer surfaces"
else
echo "Creating additional cortical layer surfaces"
LayersList=`echo ${Layers} | sed 's/@/ /g'`
LayersNameList=`echo corticallayer_${Layers} | sed 's/@/ corticallayer_/g'`
for EachLayer in $LayersList; do
${CARET7DIR}/wb_command -surface-cortex-layer "$Folder"/"$Subject"."$Hemisphere".white.native.surf.gii "$Folder"/"$Subject"."$Hemisphere".pial.native.surf.gii "$EachLayer" "$Folder"/"$Subject"."$Hemisphere".corticallayer_"$EachLayer".native.surf.gii
${CARET7DIR}/wb_command -set-structure "$Folder"/"$Subject"."$Hemisphere".corticallayer_"$EachLayer".native.surf.gii ${Structure} -surface-type ANATOMICAL -surface-secondary-type INVALID
${CARET7DIR}/wb_command -add-to-spec-file "$Folder"/"$Subject".native.wb.spec $Structure ./"$Subject"."$Hemisphere".corticallayer_"$EachLayer".native.surf.gii
done
fi
popd > /dev/null
done
#Convert original and registered spherical surfaces and add them to the spec file
for Surface in sphere.reg sphere ; do
mris_convert "$FreeSurferFolder"/surf/"$hemisphere"h."$Surface" "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
${CARET7DIR}/wb_command -set-structure "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${Structure} -surface-type SPHERICAL
done
pushd > /dev/null "$HCPFolder"
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject".native.wb.spec $Structure ./"$Subject"."$Hemisphere".sphere.native.surf.gii
popd > /dev/null
#Add more files to the spec file and convert other FreeSurfer surface data to metric/GIFTI including sulc, curv, and thickness.
for Map in sulc@sulc@Sulc thickness@thickness@Thickness curv@curvature@Curvature ; do
fsname=`echo $Map | cut -d "@" -f 1`
wbname=`echo $Map | cut -d "@" -f 2`
mapname=`echo $Map | cut -d "@" -f 3`
mris_convert -c "$FreeSurferFolder"/surf/"$hemisphere"h."$fsname" "$FreeSurferFolder"/surf/"$hemisphere"h.white "$HCPFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii
${CARET7DIR}/wb_command -set-structure "$HCPFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii ${Structure}
${CARET7DIR}/wb_command -metric-math "var * -1" "$HCPFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii -var var "$HCPFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii
${CARET7DIR}/wb_command -set-map-names "$HCPFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii -map 1 "$Subject"_"$Hemisphere"_"$mapname"
${CARET7DIR}/wb_command -metric-palette "$HCPFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii MODE_AUTO_SCALE_PERCENTAGE -pos-percent 2 98 -palette-name Gray_Interp -disp-pos true -disp-neg true -disp-zero true
done
#Thickness specific operations (we should review the implications of the math...)
${CARET7DIR}/wb_command -metric-math "abs(thickness)" "$HCPFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii -var thickness "$HCPFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
${CARET7DIR}/wb_command -metric-palette "$HCPFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii MODE_AUTO_SCALE_PERCENTAGE -pos-percent 4 96 -interpolate true -palette-name videen_style -disp-pos true -disp-neg false -disp-zero false
${CARET7DIR}/wb_command -metric-math "thickness > 0" "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -var thickness "$HCPFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
${CARET7DIR}/wb_command -metric-fill-holes "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
${CARET7DIR}/wb_command -metric-remove-islands "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
${CARET7DIR}/wb_command -set-map-names "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -map 1 "$Subject"_"$Hemisphere"_ROI
${CARET7DIR}/wb_command -metric-dilate "$HCPFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii 10 "$HCPFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii -nearest
${CARET7DIR}/wb_command -metric-dilate "$HCPFolder"/"$Subject"."$Hemisphere".curvature.native.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii 10 "$HCPFolder"/"$Subject"."$Hemisphere".curvature.native.shape.gii -nearest
#Label operations
for Map in aparc aparc.a2009s BA ; do
if [ -e "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot ] ; then
mris_convert --annot "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot "$FreeSurferFolder"/surf/"$hemisphere"h.white "$HCPFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii
${CARET7DIR}/wb_command -set-structure "$HCPFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii $Structure
${CARET7DIR}/wb_command -set-map-names "$HCPFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii -map 1 "$Subject"_"$Hemisphere"_"$Map"
${CARET7DIR}/wb_command -gifti-label-add-prefix "$HCPFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii "${Hemisphere}_" "$HCPFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii
fi
done
#End main native mesh processing
#Copy Atlas Files
if [ ! -e "$HCPFolder"/fsaverage ] ; then
mkdir -p "$HCPFolder"/fsaverage
fi
cp "$SurfaceAtlasDIR"/fs_"$Hemisphere"/fsaverage."$Hemisphere".sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii "$HCPFolder"/fsaverage/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii
cp "$SurfaceAtlasDIR"/fs_"$Hemisphere"/fs_"$Hemisphere"-to-fs_LR_fsaverage."$Hemisphere"_LR.spherical_std."$HighResMesh"k_fs_"$Hemisphere".surf.gii "$HCPFolder"/fsaverage/"$Subject"."$Hemisphere".def_sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii
cp "$SurfaceAtlasDIR"/fsaverage."$Hemisphere"_LR.spherical_std."$HighResMesh"k_fs_LR.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii
pushd > /dev/null "$HCPFolder"
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii
popd > /dev/null
cp "$SurfaceAtlasDIR"/"$Hemisphere".atlasroi."$HighResMesh"k_fs_LR.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".roi."$HighResMesh"k_fs_LR.shape.gii
cp "$SurfaceAtlasDIR"/"$Hemisphere".refsulc."$HighResMesh"k_fs_LR.shape.gii "$HCPFolder"/${Subject}.${Hemisphere}.refsulc."$HighResMesh"k_fs_LR.shape.gii
if [ -e "$SurfaceAtlasDIR"/colin.cerebral."$Hemisphere".flat."$HighResMesh"k_fs_LR.surf.gii ] ; then
cp "$SurfaceAtlasDIR"/colin.cerebral."$Hemisphere".flat."$HighResMesh"k_fs_LR.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".flat."$HighResMesh"k_fs_LR.surf.gii
pushd > /dev/null "$HCPFolder"
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere".flat."$HighResMesh"k_fs_LR.surf.gii
popd > /dev/null
fi
#Concatinate FS registration to FS --> FS_LR registration
${CARET7DIR}/wb_command -surface-sphere-project-unproject "$HCPFolder"/"$Subject"."$Hemisphere".sphere.reg.native.surf.gii "$HCPFolder"/fsaverage/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii "$HCPFolder"/fsaverage/"$Subject"."$Hemisphere".def_sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.surf.gii
#Make FreeSurfer Registration Areal Distortion Maps
${CARET7DIR}/wb_command -surface-vertex-areas "$HCPFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii
${CARET7DIR}/wb_command -surface-vertex-areas "$HCPFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.shape.gii
${CARET7DIR}/wb_command -metric-math "ln(spherereg / sphere) / ln(2)" "$HCPFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii -var sphere "$HCPFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii -var spherereg "$HCPFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.shape.gii
rm "$HCPFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.shape.gii
${CARET7DIR}/wb_command -set-map-names "$HCPFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii -map 1 "$Subject"_"$Hemisphere"_Areal_Distortion_FS
${CARET7DIR}/wb_command -metric-palette "$HCPFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii MODE_AUTO_SCALE -palette-name ROY-BIG-BL -thresholding THRESHOLD_TYPE_NORMAL THRESHOLD_TEST_SHOW_OUTSIDE -1 1
RegSphere="${HCPFolder}/${Subject}.${Hemisphere}.sphere.reg.reg_LR.native.surf.gii"
#Ensure no zeros in atlas medial wall ROI
${CARET7DIR}/wb_command -metric-resample "$HCPFolder"/"$Subject"."$Hemisphere".roi."$HighResMesh"k_fs_LR.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ${RegSphere} BARYCENTRIC "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -largest
${CARET7DIR}/wb_command -metric-math "(atlas + individual) > 0" "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -var atlas "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -var individual "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
${CARET7DIR}/wb_command -metric-mask "$HCPFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
${CARET7DIR}/wb_command -metric-mask "$HCPFolder"/"$Subject"."$Hemisphere".curvature.native.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".curvature.native.shape.gii
#Populate Highres fs_LR spec file. Deform surfaces and other data according to native to folding-based registration selected above. Regenerate inflated surfaces.
for Surface in white midthickness pial $LayersNameList $SubcortNameList; do
${CARET7DIR}/wb_command -surface-resample "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${RegSphere} "$HCPFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii BARYCENTRIC "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface"."$HighResMesh"k_fs_LR.surf.gii
pushd > /dev/null "$HCPFolder"
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere"."$Surface"."$HighResMesh"k_fs_LR.surf.gii
popd > /dev/null
done
${CARET7DIR}/wb_command -surface-generate-inflated "$HCPFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".inflated."$HighResMesh"k_fs_LR.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".very_inflated."$HighResMesh"k_fs_LR.surf.gii -iterations-scale 2.5
pushd > /dev/null "$HCPFolder"
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere".inflated."$HighResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere".very_inflated."$HighResMesh"k_fs_LR.surf.gii
popd > /dev/null
for Map in thickness curvature ; do
${CARET7DIR}/wb_command -metric-resample "$HCPFolder"/"$Subject"."$Hemisphere"."$Map".native.shape.gii ${RegSphere} "$HCPFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$HCPFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii -current-roi "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
${CARET7DIR}/wb_command -metric-mask "$HCPFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".roi."$HighResMesh"k_fs_LR.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.shape.gii
done
${CARET7DIR}/wb_command -metric-resample "$HCPFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii ${RegSphere} "$HCPFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$HCPFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -metric-resample "$HCPFolder"/"$Subject"."$Hemisphere".sulc.native.shape.gii ${RegSphere} "$HCPFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$HCPFolder"/"$Subject"."$Hemisphere".sulc."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
for Map in aparc aparc.a2009s BA ; do
if [ -e "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot ] ; then
${CARET7DIR}/wb_command -label-resample "$HCPFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii ${RegSphere} "$HCPFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii BARYCENTRIC "$HCPFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.label.gii -largest
fi
done
for LowResMesh in ${LowResMeshes} ; do
if [ ! -e "$HCPFolder"/fsaverage_LR"$LowResMesh"k ] ; then
mkdir -p "$HCPFolder"/fsaverage_LR"$LowResMesh"k
fi
for Image in $Target ; do
pushd > /dev/null "$HCPFolder"/fsaverage_LR"$LowResMesh"k
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID ../"$Image".nii.gz
popd > /dev/null
done
#Copy Atlas Files
pushd > /dev/null "$HCPFolder"/fsaverage_LR"$LowResMesh"k
cp "$SurfaceAtlasDIR"/"$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii
cp "$GrayordinatesSpaceDIR"/"$Hemisphere".atlasroi."$LowResMesh"k_fs_LR.shape.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".roi."$LowResMesh"k_fs_LR.shape.gii
if [ -e "$SurfaceAtlasDIR"/colin.cerebral."$Hemisphere".flat."$LowResMesh"k_fs_LR.surf.gii ] ; then
cp "$SurfaceAtlasDIR"/colin.cerebral."$Hemisphere".flat."$LowResMesh"k_fs_LR.surf.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".flat."$LowResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere".flat."$LowResMesh"k_fs_LR.surf.gii
fi
#Create downsampled fs_LR spec files.
for Surface in white midthickness pial $LayersNameList $SubcortNameList; do
${CARET7DIR}/wb_command -surface-resample "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${RegSphere} "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii BARYCENTRIC "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Surface"."$LowResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere"."$Surface"."$LowResMesh"k_fs_LR.surf.gii
done
${CARET7DIR}/wb_command -surface-generate-inflated "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".inflated."$LowResMesh"k_fs_LR.surf.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".very_inflated."$LowResMesh"k_fs_LR.surf.gii -iterations-scale 0.75
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere".inflated."$LowResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere".very_inflated."$LowResMesh"k_fs_LR.surf.gii
popd > /dev/null
for Map in sulc thickness curvature ; do
${CARET7DIR}/wb_command -metric-resample "$HCPFolder"/"$Subject"."$Hemisphere"."$Map".native.shape.gii ${RegSphere} "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii -current-roi "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
${CARET7DIR}/wb_command -metric-mask "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.shape.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".roi."$LowResMesh"k_fs_LR.shape.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.shape.gii
done
${CARET7DIR}/wb_command -metric-resample "$HCPFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii ${RegSphere} "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".ArealDistortion_FS."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -metric-resample "$HCPFolder"/"$Subject"."$Hemisphere".sulc.native.shape.gii ${RegSphere} "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sulc."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
for Map in aparc aparc.a2009s BA ; do
if [ -e "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot ] ; then
${CARET7DIR}/wb_command -label-resample "$HCPFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii ${RegSphere} "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii BARYCENTRIC "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.label.gii -largest
fi
done
done
done
STRINGII=""
for LowResMesh in ${LowResMeshes} ; do
STRINGII=`echo "${STRINGII}${HCPFolder}/fsaverage_LR${LowResMesh}k@${LowResMesh}k_fs_LR@roi "`
done
#Create CIFTI Files
for STRING in "$HCPFolder"@native@roi "$HCPFolder"@"$HighResMesh"k_fs_LR@roi ${STRINGII} ; do
Folder=`echo $STRING | cut -d "@" -f 1`
Mesh=`echo $STRING | cut -d "@" -f 2`
ROI=`echo $STRING | cut -d "@" -f 3`
${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".sulc."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.sulc."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.sulc."$Mesh".shape.gii
${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".sulc."$Mesh".dscalar.nii -map 1 "${Subject}_Sulc"
${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".sulc."$Mesh".dscalar.nii MODE_AUTO_SCALE_PERCENTAGE "$Folder"/"$Subject".sulc."$Mesh".dscalar.nii -pos-percent 2 98 -palette-name Gray_Interp -disp-pos true -disp-neg true -disp-zero true
${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".curvature."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.curvature."$Mesh".shape.gii -roi-left "$Folder"/"$Subject".L."$ROI"."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.curvature."$Mesh".shape.gii -roi-right "$Folder"/"$Subject".R."$ROI"."$Mesh".shape.gii
${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".curvature."$Mesh".dscalar.nii -map 1 "${Subject}_Curvature"
${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".curvature."$Mesh".dscalar.nii MODE_AUTO_SCALE_PERCENTAGE "$Folder"/"$Subject".curvature."$Mesh".dscalar.nii -pos-percent 2 98 -palette-name Gray_Interp -disp-pos true -disp-neg true -disp-zero true
${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".thickness."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.thickness."$Mesh".shape.gii -roi-left "$Folder"/"$Subject".L."$ROI"."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.thickness."$Mesh".shape.gii -roi-right "$Folder"/"$Subject".R."$ROI"."$Mesh".shape.gii
${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".thickness."$Mesh".dscalar.nii -map 1 "${Subject}_Thickness"
${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".thickness."$Mesh".dscalar.nii MODE_AUTO_SCALE_PERCENTAGE "$Folder"/"$Subject".thickness."$Mesh".dscalar.nii -pos-percent 4 96 -interpolate true -palette-name videen_style -disp-pos true -disp-neg false -disp-zero false
${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".ArealDistortion_FS."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.ArealDistortion_FS."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.ArealDistortion_FS."$Mesh".shape.gii
${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".ArealDistortion_FS."$Mesh".dscalar.nii -map 1 "${Subject}_ArealDistortion_FS"
${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".ArealDistortion_FS."$Mesh".dscalar.nii MODE_USER_SCALE "$Folder"/"$Subject".ArealDistortion_FS."$Mesh".dscalar.nii -pos-user 0 1 -neg-user 0 -1 -interpolate true -palette-name ROY-BIG-BL -disp-pos true -disp-neg true -disp-zero false
for Map in aparc aparc.a2009s BA ; do
if [ -e "$Folder"/"$Subject".L.${Map}."$Mesh".label.gii ] ; then
${CARET7DIR}/wb_command -cifti-create-label "$Folder"/"$Subject".${Map}."$Mesh".dlabel.nii -left-label "$Folder"/"$Subject".L.${Map}."$Mesh".label.gii -roi-left "$Folder"/"$Subject".L."$ROI"."$Mesh".shape.gii -right-label "$Folder"/"$Subject".R.${Map}."$Mesh".label.gii -roi-right "$Folder"/"$Subject".R."$ROI"."$Mesh".shape.gii
${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".${Map}."$Mesh".dlabel.nii -map 1 "$Subject"_${Map}
fi
done
done
STRINGII=""
for LowResMesh in ${LowResMeshes} ; do
STRINGII=`echo "${STRINGII}${HCPFolder}/fsaverage_LR${LowResMesh}k@${HCPFolder}/fsaverage_LR${LowResMesh}k@${LowResMesh}k_fs_LR"`
done
#Add CIFTI Maps to Spec Files
for STRING in "$HCPFolder"@"$HCPFolder"@native "$HCPFolder"@"$HCPFolder"@"$HighResMesh"k_fs_LR ${STRINGII} ; do
FolderI=`echo $STRING | cut -d "@" -f 1`
FolderII=`echo $STRING | cut -d "@" -f 2`
Mesh=`echo $STRING | cut -d "@" -f 3`
for STRINGII in sulc@dscalar thickness@dscalar curvature@dscalar aparc@dlabel aparc.a2009s@dlabel BA@dlabel ; do
Map=`echo $STRINGII | cut -d "@" -f 1`
Ext=`echo $STRINGII | cut -d "@" -f 2`
if [ -e "$FolderII"/"$Subject"."$Map"."$Mesh"."$Ext".nii ] ; then
pushd > /dev/null "$FolderI"
${CARET7DIR}/wb_command -add-to-spec-file "$FolderI"/"$Subject"."$Mesh".wb.spec INVALID ./"$Subject"."$Map"."$Mesh"."$Ext".nii
popd > /dev/null
fi
done
done