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FreeSurfer2Workbench.sh
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FreeSurfer2Workbench.sh
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#!/bin/bash
# ------------------------------------------------------------------------------
# Code Start
# ------------------------------------------------------------------------------
# Setup this script such that if any command exits with a non-zero value, the
# script itself exits and does not attempt any further processing.
set -e
set -x
# ------------------------------------------------------------------------------
# Load Function Libraries
# ------------------------------------------------------------------------------
#Set up pipeline environment variables and software
module load FSL/5.0.7 freesurfer/5.3.0 connectome-workbench/1.1.1 hcp-pipelines/3.7.0
source $HCPPIPEDIR/global/scripts/log.shlib # Logging related functions
source $HCPPIPEDIR/global/scripts/opts.shlib # Command line option functions
# ------------------------------------------------------------------------------
# Usage Description Function
# ------------------------------------------------------------------------------
show_usage() {
cat <<EOF
FreeSurfer2Workbench.sh
Usage: FreeSurfer2Workbench.sh --FSpath=<path> --HCPpath=<path> --subject=<subject>
--FSpath=<path> Path to study data freesurfer study folder (required)
--HCPpath=<path> Path to the study hcp data folder
--subject=<subject> Subject ID (required)
Used with --path input to create full path to root
directory for all outputs generated as path/subject
EOF
exit 1
}
# ------------------------------------------------------------------------------
# Establish tool name for logging
# ------------------------------------------------------------------------------
log_SetToolName "FreeSurfer2Workbench.sh"
# ------------------------------------------------------------------------------
# Parse Command Line Options
# ------------------------------------------------------------------------------
opts_ShowVersionIfRequested $@
if opts_CheckForHelpRequest $@; then
show_usage
fi
log_Msg "Platform Information Follows: "
uname -a
log_Msg "Parsing Command Line Options"
FSFolder=`opts_GetOpt1 "--FSpath" $@`
HCPFolder=`opts_GetOpt1 "--HCPpath" $@`
Subject=`opts_GetOpt1 "--subject" $@`
# Use --printcom=echo for just printing everything and not actually
# running the commands (the default is to actually run the commands)
RUN=`opts_GetOpt1 "--printcom" $@`
# ------------------------------------------------------------------------------
# Show Command Line Options
# ------------------------------------------------------------------------------
log_Msg "Finished Parsing Command Line Options"
log_Msg "Freesurfer Folder: ${FSFolder}"
log_Msg "HCP Folder: ${HCPFolder}"
log_Msg "Subject: ${Subject}"
echo -e "\n START: FS2CaretConvertRegisterNonlinear"
###Templates and settings
BrainSize="150" #BrainSize in mm, 150 for humans
FNIRTConfig="${HCPPIPEDIR_Config}/T1_2_MNI152_2mm.cnf" #FNIRT 2mm T1w Config
T1wTemplate="${HCPPIPEDIR_Templates}/MNI152_T1_1mm.nii.gz" #Hires T1w MNI template
T1wTemplateBrain="${HCPPIPEDIR_Templates}/MNI152_T1_1mm_brain.nii.gz" #Hires brain extracted MNI template
T1wTemplate2mm="${HCPPIPEDIR_Templates}/MNI152_T1_2mm.nii.gz" #Lowres T1w MNI template
T1wTemplateMask="${HCPPIPEDIR_Templates}/MNI152_T1_1mm_brain_mask.nii.gz" #Hires MNI brain mask template
T1wTemplate2mmMask="${HCPPIPEDIR_Templates}/MNI152_T1_2mm_brain_mask_dil.nii.gz" #Lowres MNI brain mask template
FreeSurferLabels="${HCPPIPEDIR_Config}/FreeSurferAllLut.txt"
GrayordinatesSpaceDIR="${HCPPIPEDIR_Templates}/91282_Greyordinates"
SubcorticalGrayLabels="${HCPPIPEDIR_Config}/FreeSurferSubcorticalLabelTableLut.txt"
SurfaceAtlasDIR="${HCPPIPEDIR_Templates}/standard_mesh_atlases"
### Naming conventions
AtlasSpaceFolder="$HCPFolder"/"$Subject"/MNINonLinear
AtlasTransform="$AtlasSpaceFolder"/xfms/acpc2standard
InverseAtlasTransform="$AtlasSpaceFolder"/xfms/standard2acpc
FeatSubjectFolder="$FeatFolder"/"$Subject.feat"
FreeSurferFolder="$FSFolder"/"$Subject"
GrayordinatesResolutions="2"
HighResMesh="164"
LowResMeshes="32"
NativeFolder="Native"
RegName="FS"
T1wImageBrainMask="brainmask_fs"
T1wFolder="$HCPFolder"/"$Subject"/"T1w"
T1w_nonacpc="T1w_noacpc"
#T1wImage="T1w_acpc" #if running ACPC
T1wImage="T1w" #if not running
#T2wImage="$9"
#Make some folders for this and later scripts
if [ ! -e "$T1wFolder"/"$NativeFolder" ] ; then
mkdir -p "$T1wFolder"/"$NativeFolder"
fi
if [ ! -e "$AtlasSpaceFolder"/xfms ] ; then
mkdir -p "$AtlasSpaceFolder"/xfms
fi
if [ ! -e "$AtlasSpaceFolder"/ROIs ] ; then
mkdir -p "$AtlasSpaceFolder"/ROIs
fi
if [ ! -e "$AtlasSpaceFolder"/Results ] ; then
mkdir "$AtlasSpaceFolder"/Results
fi
if [ ! -e "$AtlasSpaceFolder"/"$NativeFolder" ] ; then
mkdir "$AtlasSpaceFolder"/"$NativeFolder"
fi
if [ ! -e "$AtlasSpaceFolder"/fsaverage ] ; then
mkdir "$AtlasSpaceFolder"/fsaverage
fi
for LowResMesh in ${LowResMeshes} ; do
if [ ! -e "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k ] ; then
mkdir "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k
fi
if [ ! -e "$T1wFolder"/fsaverage_LR"$LowResMesh"k ] ; then
mkdir "$T1wFolder"/fsaverage_LR"$LowResMesh"k
fi
done
if [ ! -e ${T1wFolder}/xfms ] ; then
log_Msg "mkdir -p ${T1wFolder}/xfms/"
mkdir -p ${T1wFolder}/xfms/
fi
# ###### convert the mgz T1w and put in T1w folder - if running ACPC
# mri_convert "$FreeSurferFolder"/mri/T1.mgz "$T1wFolder"/${T1w_nonacpc}.nii.gz
# fslreorient2std "$T1wFolder"/${T1w_nonacpc}.nii.gz "$T1wFolder"/${T1w_nonacpc}.nii.gz
# #mri_convert "$FreeSurferFolder"/mri/brainmask.mgz "$T1wFolder"/${T1w_nonacpc}_brain_mask.nii.gz
# ##ACPC align T1w or T2w image to 1mm MNI Template to create native volume space
# log_Msg "Aligning ${T1w_nonacpc} image to ${T1w} Template to create native volume space"
# log_Msg "mkdir -p ${T1wFolder}/ACPCAlignment"
# mkdir -p ${T1wFolder}/ACPCAlignment
# ${RUN} ${HCPPIPEDIR_PreFS}/ACPCAlignment.sh \
# --workingdir=${T1wFolder}/ACPCAlignment \
# --in=${T1wFolder}/${T1w_nonacpc} \
# --ref=${T1wTemplate} \
# --out=${T1wFolder}/${T1wImage} \
# --omat=${T1wFolder}/xfms/acpc.mat \
# --brainsize=${BrainSize}
###### convert the mgz T1w and put in T1w folder
mri_convert "$FreeSurferFolder"/mri/T1.mgz "$T1wFolder"/${T1wImage}.nii.gz
fslreorient2std "$T1wFolder"/${T1wImage}.nii.gz "$T1wFolder"/${T1wImage}.nii.gz
##### Linear then non-linear registration to MNI
${FSLDIR}/bin/flirt -interp spline -dof 12 -in ${T1wFolder}/${T1wImage} -ref ${T1wTemplate} -omat ${AtlasSpaceFolder}/xfms/acpc2MNILinear.mat -out ${AtlasSpaceFolder}/xfms/${T1wImage}_to_MNILinear
${FSLDIR}/bin/fnirt --in=${T1wFolder}/${T1wImage} --ref=${T1wTemplate2mm} --aff=${AtlasSpaceFolder}/xfms/acpc2MNILinear.mat --refmask=${T1wTemplate2mmMask} --fout=${AtlasTransform}_warp --jout=${AtlasSpaceFolder}/xfms/NonlinearRegJacobians.nii.gz --refout=${AtlasSpaceFolder}/xfms/IntensityModulatedT1.nii.gz --iout=${AtlasSpaceFolder}/xfms/2mmReg.nii.gz --logout=${AtlasSpaceFolder}/xfms/NonlinearReg.txt --intout=${AtlasSpaceFolder}/xfms/NonlinearIntensities.nii.gz --cout=${AtlasSpaceFolder}/xfms/NonlinearReg.nii.gz --config=${FNIRTConfig}
### calculate the just the warp for the surface transform - need it because sometimes the brain is outside the bounding box of warfield
${FSLDIR}/bin/fnirt --in=${AtlasSpaceFolder}/xfms/${T1wImage}_to_MNILinear --ref=${T1wTemplate2mm} --refmask=${T1wTemplate2mmMask} --fout=${AtlasTransform}_warp_noaffine --logout=${AtlasSpaceFolder}/xfms/NonlinearReg_fromlinear.txt --config=${FNIRTConfig}
##Input and reference spaces are the same, using 2mm reference to save time
${FSLDIR}/bin/invwarp -w ${AtlasTransform}_warp -o ${InverseAtlasTransform}_warp -r ${T1wTemplate2mm}
## also inverse the non-prelinear warp
${FSLDIR}/bin/invwarp -w ${AtlasTransform}_warp_noaffine -o ${InverseAtlasTransform}_warp_noaffine -r ${T1wTemplate2mm}
##T1w set of warped outputs (brain/whole-head + restored/orig)
${FSLDIR}/bin/applywarp --rel --interp=trilinear -i ${T1wFolder}/${T1wImage} -r ${T1wTemplate2mm} -w ${AtlasTransform}_warp -o ${AtlasSpaceFolder}/${T1wImage}
## also do the brainmask...but we are getting another from freesurfer anyway
#${FSLDIR}/bin/applywarp --rel --interp=nn -i ${T1wFolder}/${T1w_nonacpc}_brain_mask.nii.gz -r ${T1wTemplate2mm} -w ${AtlasTransform}_warp --premat=${T1wFolder}/xfms/acpc.mat -o ${AtlasSpaceFolder}/${T1wImage}_brain_mask
#${FSLDIR}/bin/fslmaths ${AtlasSpaceFolder}/${T1wImage} -mas ${AtlasSpaceFolder}/${T1wImage}_brain_mask ${AtlasSpaceFolder}/${T1wImage}_brain
#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
for Image in wmparc aparc.a2009s+aseg aparc+aseg ; do
if [ -e "$FreeSurferFolder"/mri/"$Image".mgz ] ; then
mri_convert -rt nearest -rl "$T1wFolder"/"$T1wImage".nii.gz "$FreeSurferFolder"/mri/"$Image".mgz "$T1wFolder"/"$Image".nii.gz
# applywarp --rel --interp=nn -i "$T1wFolder"/"$Image"_1mm.nii.gz -r "$AtlasSpaceFolder"/"$T1wImage" --premat=$FSLDIR/etc/flirtsch/ident.mat -o "$T1wFolder"/"$Image".nii.gz
# applywarp --rel --interp=nn -i "$T1wFolder"/"$Image"_1mm.nii.gz -r "$AtlasSpaceFolder"/"$T1wImage" -w "$AtlasTransform"_warp -o "$AtlasSpaceFolder"/"$Image".nii.gz
#mri_convert "$FreeSurferFolder"/mri/"$Image".mgz "$T1wFolder"/"$Image".nii.gz
applywarp --rel --interp=nn -i "$T1wFolder"/"$Image".nii.gz -r "$AtlasSpaceFolder"/"$T1wImage" -w "$AtlasTransform"_warp -o "$AtlasSpaceFolder"/"$Image".nii.gz
${CARET7DIR}/wb_command -volume-label-import "$T1wFolder"/"$Image".nii.gz "$FreeSurferLabels" "$T1wFolder"/"$Image".nii.gz -drop-unused-labels
${CARET7DIR}/wb_command -volume-label-import "$AtlasSpaceFolder"/"$Image".nii.gz "$FreeSurferLabels" "$AtlasSpaceFolder"/"$Image".nii.gz -drop-unused-labels
fi
done
# #Create FreeSurfer Brain Mask using 1mm version...
# fslmaths "$T1wFolder"/wmparc_1mm.nii.gz -bin -dilD -dilD -dilD -ero -ero "$T1wFolder"/"$T1wImageBrainMask"_1mm.nii.gz
# ${CARET7DIR}/wb_command -volume-fill-holes "$T1wFolder"/"$T1wImageBrainMask"_1mm.nii.gz "$T1wFolder"/"$T1wImageBrainMask"_1mm.nii.gz
# fslmaths "$T1wFolder"/"$T1wImageBrainMask"_1mm.nii.gz -bin "$T1wFolder"/"$T1wImageBrainMask"_1mm.nii.gz
# applywarp --rel --interp=nn -i "$T1wFolder"/"$T1wImageBrainMask"_1mm.nii.gz -r "$AtlasSpaceFolder"/"$T1wImage" --premat=$FSLDIR/etc/flirtsch/ident.mat -o "$T1wFolder"/"$T1wImageBrainMask".nii.gz
# applywarp --rel --interp=nn -i "$T1wFolder"/"$T1wImageBrainMask"_1mm.nii.gz -r "$AtlasSpaceFolder"/"$T1wImage" -w "$AtlasTransform"_warp -o "$AtlasSpaceFolder"/"$T1wImageBrainMask".nii.gz
#Create FreeSurfer Brain Mask skipping 1mm version...
fslmaths "$T1wFolder"/wmparc.nii.gz -bin -dilD -dilD -dilD -ero -ero "$T1wFolder"/"$T1wImageBrainMask".nii.gz
${CARET7DIR}/wb_command -volume-fill-holes "$T1wFolder"/"$T1wImageBrainMask".nii.gz "$T1wFolder"/"$T1wImageBrainMask".nii.gz
fslmaths "$T1wFolder"/"$T1wImageBrainMask".nii.gz -bin "$T1wFolder"/"$T1wImageBrainMask".nii.gz
applywarp --rel --interp=nn -i "$T1wFolder"/"$T1wImageBrainMask".nii.gz -r "$AtlasSpaceFolder"/"$T1wImage" --premat=$FSLDIR/etc/flirtsch/ident.mat -o "$T1wFolder"/"$T1wImageBrainMask".nii.gz
applywarp --rel --interp=nn -i "$T1wFolder"/"$T1wImageBrainMask".nii.gz -r "$AtlasSpaceFolder"/"$T1wImage" -w "$AtlasTransform"_warp -o "$AtlasSpaceFolder"/"$T1wImageBrainMask".nii.gz
#Add volume files to spec files
#${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/"$NativeFolder"/"$Subject".native.wb.spec INVALID "$T1wFolder"/"$T2wImage".nii.gz
${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/"$NativeFolder"/"$Subject".native.wb.spec INVALID "$T1wFolder"/"$T1wImage".nii.gz
#${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject".native.wb.spec INVALID "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage".nii.gz
${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject".native.wb.spec INVALID "$AtlasSpaceFolder"/"$T1wImage".nii.gz
#${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec INVALID "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage".nii.gz
${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec INVALID "$AtlasSpaceFolder"/"$T1wImage".nii.gz
for LowResMesh in ${LowResMeshes} ; do
#${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage".nii.gz
${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID "$AtlasSpaceFolder"/"$T1wImage".nii.gz
#${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID "$T1wFolder"/"$T2wImage".nii.gz
${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID "$T1wFolder"/"$T1wImage".nii.gz
done
#Import Subcortical ROIs
for GrayordinatesResolution in ${GrayordinatesResolutions} ; do
cp "$GrayordinatesSpaceDIR"/Atlas_ROIs."$GrayordinatesResolution".nii.gz "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz
applywarp --interp=nn -i "$AtlasSpaceFolder"/wmparc.nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/ROIs/wmparc."$GrayordinatesResolution".nii.gz
${CARET7DIR}/wb_command -volume-label-import "$AtlasSpaceFolder"/ROIs/wmparc."$GrayordinatesResolution".nii.gz "$FreeSurferLabels" "$AtlasSpaceFolder"/ROIs/wmparc."$GrayordinatesResolution".nii.gz -drop-unused-labels
applywarp --interp=nn -i "$SurfaceAtlasDIR"/Avgwmparc.nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/ROIs/Atlas_wmparc."$GrayordinatesResolution".nii.gz
${CARET7DIR}/wb_command -volume-label-import "$AtlasSpaceFolder"/ROIs/Atlas_wmparc."$GrayordinatesResolution".nii.gz "$FreeSurferLabels" "$AtlasSpaceFolder"/ROIs/Atlas_wmparc."$GrayordinatesResolution".nii.gz -drop-unused-labels
${CARET7DIR}/wb_command -volume-label-import "$AtlasSpaceFolder"/ROIs/wmparc."$GrayordinatesResolution".nii.gz ${SubcorticalGrayLabels} "$AtlasSpaceFolder"/ROIs/ROIs."$GrayordinatesResolution".nii.gz -discard-others
#applywarp --interp=spline -i "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage".nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage"."$GrayordinatesResolution".nii.gz
applywarp --interp=spline -i "$AtlasSpaceFolder"/"$T1wImage".nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/"$T1wImage"."$GrayordinatesResolution".nii.gz
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
mris_convert "$FreeSurferFolder"/surf/"$hemisphere"h."$Surface" "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
${CARET7DIR}/wb_command -set-structure "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${Structure} -surface-type $Type$Secondary
${CARET7DIR}/wb_command -surface-apply-affine "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii "$FreeSurferFolder"/mri/c_ras.mat "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
${CARET7DIR}/wb_command -surface-apply-affine "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${AtlasSpaceFolder}/xfms/acpc2MNILinear.mat "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii -flirt ${T1wFolder}/${T1wImage}.nii.gz ${T1wTemplate}
${CARET7DIR}/wb_command -surface-apply-warpfield "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii "${InverseAtlasTransform}"_warp_noaffine.nii.gz "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii -fnirt "$AtlasTransform"_warp_noaffine.nii.gz
${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
i=$(($i+1))
done
#Create midthickness by averaging white and pial surfaces and use it to make inflated surfacess
for Folder in "$T1wFolder" "$AtlasSpaceFolder" ; do
${CARET7DIR}/wb_command -surface-average "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii -surf "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".white.native.surf.gii -surf "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".pial.native.surf.gii
${CARET7DIR}/wb_command -set-structure "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii ${Structure} -surface-type ANATOMICAL -surface-secondary-type MIDTHICKNESS
${CARET7DIR}/wb_command -add-to-spec-file "$Folder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii
${CARET7DIR}/wb_command -surface-generate-inflated "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".inflated.native.surf.gii "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".very_inflated.native.surf.gii -iterations-scale 2.5
${CARET7DIR}/wb_command -add-to-spec-file "$Folder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".inflated.native.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$Folder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".very_inflated.native.surf.gii
done
#Convert original and registered spherical surfaces and add them to the nonlinear spec file
for Surface in sphere.reg sphere ; do
mris_convert "$FreeSurferFolder"/surf/"$hemisphere"h."$Surface" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
${CARET7DIR}/wb_command -set-structure "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${Structure} -surface-type SPHERICAL
done
${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii
#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 "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii
${CARET7DIR}/wb_command -set-structure "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii ${Structure}
${CARET7DIR}/wb_command -metric-math "var * -1" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii -var var "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii
${CARET7DIR}/wb_command -set-map-names "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii -map 1 "$Subject"_"$Hemisphere"_"$mapname"
${CARET7DIR}/wb_command -metric-palette "$AtlasSpaceFolder"/"$NativeFolder"/"$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
${CARET7DIR}/wb_command -metric-math "abs(thickness)" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii -var thickness "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
${CARET7DIR}/wb_command -metric-palette "$AtlasSpaceFolder"/"$NativeFolder"/"$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
${CARET7DIR}/wb_command -metric-math "thickness > 0" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -var thickness "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
${CARET7DIR}/wb_command -metric-fill-holes "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
${CARET7DIR}/wb_command -metric-remove-islands "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
${CARET7DIR}/wb_command -set-map-names "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -map 1 "$Subject"_"$Hemisphere"_ROI
${CARET7DIR}/wb_command -metric-dilate "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii 10 "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii -nearest
${CARET7DIR}/wb_command -metric-dilate "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".curvature.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii 10 "$AtlasSpaceFolder"/"$NativeFolder"/"$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/"$hemisphere"h.white "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii
${CARET7DIR}/wb_command -set-structure "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii $Structure
${CARET7DIR}/wb_command -set-map-names "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii -map 1 "$Subject"_"$Hemisphere"_"$Map"
${CARET7DIR}/wb_command -gifti-label-add-prefix "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii "${Hemisphere}_" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii
fi
done
#End main native mesh processing
#Copy Atlas Files
cp "$SurfaceAtlasDIR"/fs_"$Hemisphere"/fsaverage."$Hemisphere".sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii "$AtlasSpaceFolder"/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 "$AtlasSpaceFolder"/fsaverage/"$Subject"."$Hemisphere".def_sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii
cp "$SurfaceAtlasDIR"/fsaverage."$Hemisphere"_LR.spherical_std."$HighResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii
cp "$SurfaceAtlasDIR"/"$Hemisphere".atlasroi."$HighResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".atlasroi."$HighResMesh"k_fs_LR.shape.gii
cp "$SurfaceAtlasDIR"/"$Hemisphere".refsulc."$HighResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/${Subject}.${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."$HighResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".flat."$HighResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".flat."$HighResMesh"k_fs_LR.surf.gii
fi
#Concatinate FS registration to FS --> FS_LR registration
${CARET7DIR}/wb_command -surface-sphere-project-unproject "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.native.surf.gii "$AtlasSpaceFolder"/fsaverage/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii "$AtlasSpaceFolder"/fsaverage/"$Subject"."$Hemisphere".def_sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.surf.gii
#Make FreeSurfer Registration Areal Distortion Maps
${CARET7DIR}/wb_command -surface-vertex-areas "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii
${CARET7DIR}/wb_command -surface-vertex-areas "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.shape.gii
${CARET7DIR}/wb_command -metric-math "ln(spherereg / sphere) / ln(2)" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii -var sphere "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii -var spherereg "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.shape.gii
rm "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.shape.gii
${CARET7DIR}/wb_command -set-map-names "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii -map 1 "$Subject"_"$Hemisphere"_Areal_Distortion_FS
${CARET7DIR}/wb_command -metric-palette "$AtlasSpaceFolder"/"$NativeFolder"/"$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
#If desired, run MSMSulc folding-based registration to FS_LR initialized with FS affine
if [ ${RegName} = "MSMSulc" ] ; then
#Calculate Affine Transform and Apply
if [ ! -e "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc ] ; then
mkdir "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc
fi
${CARET7DIR}/wb_command -surface-affine-regression "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.reg.reg_LR.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.mat
${CARET7DIR}/wb_command -surface-apply-affine "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.mat "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.sphere_rot.surf.gii
${CARET7DIR}/wb_command -surface-modify-sphere "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.sphere_rot.surf.gii 100 "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.sphere_rot.surf.gii
cp "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.sphere_rot.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii
DIR=`pwd`
cd "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc
#Register using FreeSurfer Sulc Folding Map Using MSM Algorithm Configured for Reduced Distortion
#${MSMBin}/msm --version
${MSMBin}/msm --levels=4 --conf=${MSMBin}/allparameterssulcDRconf --inmesh="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii --trans="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii --refmesh="$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii --indata="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sulc.native.shape.gii --refdata="$AtlasSpaceFolder"/${Subject}.${Hemisphere}.refsulc."$HighResMesh"k_fs_LR.shape.gii --out="$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}. --verbose
cd $DIR
cp "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.HIGHRES_transformed.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii
${CARET7DIR}/wb_command -set-structure "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii ${Structure}
#Make MSMSulc Registration Areal Distortion Maps
${CARET7DIR}/wb_command -surface-vertex-areas "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii
${CARET7DIR}/wb_command -surface-vertex-areas "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.shape.gii
${CARET7DIR}/wb_command -metric-math "ln(spherereg / sphere) / ln(2)" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc.native.shape.gii -var sphere "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii -var spherereg "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.shape.gii
rm "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.shape.gii
${CARET7DIR}/wb_command -set-map-names "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc.native.shape.gii -map 1 "$Subject"_"$Hemisphere"_Areal_Distortion_MSMSulc
${CARET7DIR}/wb_command -metric-palette "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc.native.shape.gii MODE_AUTO_SCALE -palette-name ROY-BIG-BL -thresholding THRESHOLD_TYPE_NORMAL THRESHOLD_TEST_SHOW_OUTSIDE -1 1
RegSphere="${AtlasSpaceFolder}/${NativeFolder}/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii"
else
RegSphere="${AtlasSpaceFolder}/${NativeFolder}/${Subject}.${Hemisphere}.sphere.reg.reg_LR.native.surf.gii"
fi
#Ensure no zeros in atlas medial wall ROI
${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".atlasroi."$HighResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ${RegSphere} BARYCENTRIC "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".atlasroi.native.shape.gii -largest
${CARET7DIR}/wb_command -metric-math "(atlas + individual) > 0" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -var atlas "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".atlasroi.native.shape.gii -var individual "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
${CARET7DIR}/wb_command -metric-mask "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
${CARET7DIR}/wb_command -metric-mask "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".curvature.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$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 ; do
${CARET7DIR}/wb_command -surface-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii BARYCENTRIC "$AtlasSpaceFolder"/"$Subject"."$Hemisphere"."$Surface"."$HighResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/"$Subject"."$Hemisphere"."$Surface"."$HighResMesh"k_fs_LR.surf.gii
done
${CARET7DIR}/wb_command -surface-generate-inflated "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".inflated."$HighResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".very_inflated."$HighResMesh"k_fs_LR.surf.gii -iterations-scale 2.5
${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".inflated."$HighResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".very_inflated."$HighResMesh"k_fs_LR.surf.gii
for Map in thickness curvature ; do
${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii -current-roi "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
${CARET7DIR}/wb_command -metric-mask "$AtlasSpaceFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".atlasroi."$HighResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.shape.gii
done
${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
if [ ${RegName} = "MSMSulc" ] ; then
${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
fi
${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sulc."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$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
${CARET7DIR}/wb_command -label-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii BARYCENTRIC "$AtlasSpaceFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.label.gii -largest
fi
done
for LowResMesh in ${LowResMeshes} ; do
#Copy Atlas Files
cp "$SurfaceAtlasDIR"/"$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii
cp "$GrayordinatesSpaceDIR"/"$Hemisphere".atlasroi."$LowResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".atlasroi."$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 "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".flat."$LowResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".flat."$LowResMesh"k_fs_LR.surf.gii
fi
#Create downsampled fs_LR spec files.
for Surface in white midthickness pial ; do
${CARET7DIR}/wb_command -surface-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii BARYCENTRIC "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Surface"."$LowResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Surface"."$LowResMesh"k_fs_LR.surf.gii
done
${CARET7DIR}/wb_command -surface-generate-inflated "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".inflated."$LowResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".very_inflated."$LowResMesh"k_fs_LR.surf.gii -iterations-scale 0.75
${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".inflated."$LowResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".very_inflated."$LowResMesh"k_fs_LR.surf.gii
for Map in sulc thickness curvature ; do
${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii -current-roi "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
${CARET7DIR}/wb_command -metric-mask "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".atlasroi."$LowResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.shape.gii
done
${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".ArealDistortion_FS."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
if [ ${RegName} = "MSMSulc" ] ; then
${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
fi
${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sulc."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/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
${CARET7DIR}/wb_command -label-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii BARYCENTRIC "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.label.gii -largest
fi
done
#Create downsampled fs_LR spec file in structural space.
for Surface in white midthickness pial ; do
${CARET7DIR}/wb_command -surface-resample "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii BARYCENTRIC "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Surface"."$LowResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Surface"."$LowResMesh"k_fs_LR.surf.gii
done
${CARET7DIR}/wb_command -surface-generate-inflated "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".inflated."$LowResMesh"k_fs_LR.surf.gii "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".very_inflated."$LowResMesh"k_fs_LR.surf.gii -iterations-scale 0.75
${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".inflated."$LowResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".very_inflated."$LowResMesh"k_fs_LR.surf.gii
done
done
STRINGII=""
for LowResMesh in ${LowResMeshes} ; do
STRINGII=`echo "${STRINGII}${AtlasSpaceFolder}/fsaverage_LR${LowResMesh}k@${LowResMesh}k_fs_LR@atlasroi "`
done
#Create CIFTI Files
for STRING in "$AtlasSpaceFolder"/"$NativeFolder"@native@roi "$AtlasSpaceFolder"@"$HighResMesh"k_fs_LR@atlasroi ${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
if [ ${RegName} = "MSMSulc" ] ; then
${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".ArealDistortion_MSMSulc."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.ArealDistortion_MSMSulc."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.ArealDistortion_MSMSulc."$Mesh".shape.gii
${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".ArealDistortion_MSMSulc."$Mesh".dscalar.nii -map 1 "${Subject}_ArealDistortion_MSMSulc"
${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".ArealDistortion_MSMSulc."$Mesh".dscalar.nii MODE_USER_SCALE "$Folder"/"$Subject".ArealDistortion_MSMSulc."$Mesh".dscalar.nii -pos-user 0 1 -neg-user 0 -1 -interpolate true -palette-name ROY-BIG-BL -disp-pos true -disp-neg true -disp-zero false
fi
for Map in aparc aparc.a2009s BA ; do
if [ -e "$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}${AtlasSpaceFolder}/fsaverage_LR${LowResMesh}k@${AtlasSpaceFolder}/fsaverage_LR${LowResMesh}k@${LowResMesh}k_fs_LR ${T1wFolder}/fsaverage_LR${LowResMesh}k@${AtlasSpaceFolder}/fsaverage_LR${LowResMesh}k@${LowResMesh}k_fs_LR "`
done
#Add CIFTI Maps to Spec Files
for STRING in "$T1wFolder"/"$NativeFolder"@"$AtlasSpaceFolder"/"$NativeFolder"@native "$AtlasSpaceFolder"/"$NativeFolder"@"$AtlasSpaceFolder"/"$NativeFolder"@native "$AtlasSpaceFolder"@"$AtlasSpaceFolder"@"$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
${CARET7DIR}/wb_command -add-to-spec-file "$FolderI"/"$Subject"."$Mesh".wb.spec INVALID "$FolderII"/"$Subject"."$Map"."$Mesh"."$Ext".nii
fi
done
done
echo -e "\n END: FS2CaretConvertRegisterNonlinear"