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Stand Alone MSMSulc.sh script #290

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Stand Alone MSMSulc.sh script #290

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ef0b056
Create MSMSulc.sh
nagedem Apr 9, 2024
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removed if conditional, adjusted indentations, removed redundant rota…
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Update global/scripts/MSMSulc.sh
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removed rotated sphere generation from MSMSulc.sh, run MSMSulc.sh in …
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updated MSMSulc.sh
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Update FreeSurfer2CaretConvertAndRegisterNonlinear.sh
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Update MSMSulc.sh
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Merge branch 'master' of https://github.com/nagedem/HCPpipelines
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Update FreeSurfer2CaretConvertAndRegisterNonlinear.sh
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set B for both hemispheres
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39 changes: 5 additions & 34 deletions PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh
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Expand Up @@ -414,44 +414,15 @@ for Hemisphere in L R ; do

#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
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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
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DIR=$(pwd)
cd "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc
#Register using FreeSurfer Sulc Folding Map Using MSM Algorithm Configured for Reduced Distortion
#${MSMBINDIR}/msm --version
#${MSMBINDIR}/msm --levels=4 --conf=${MSMCONFIGDIR}/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
${MSMBINDIR}/msm --conf=${MSMCONFIGDIR}/MSMSulcStrainFinalconf --inmesh="$AtlasSpaceFolder"/"$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
cp ${MSMCONFIGDIR}/MSMSulcStrainFinalconf "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.logdir/conf
cd $DIR
#cp "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.HIGHRES_transformed.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii
cp "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.sphere.reg.surf.gii "$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

${CARET7DIR}/wb_command -surface-distortion "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.MSMSulc.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".EdgeDistortion_MSMSulc.native.shape.gii -edge-method

${CARET7DIR}/wb_command -surface-distortion "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.MSMSulc.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_MSMSulc.native.shape.gii -local-affine-method
${CARET7DIR}/wb_command -metric-merge "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_MSMSulc.native.shape.gii -metric "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_MSMSulc.native.shape.gii -column 1
${CARET7DIR}/wb_command -metric-merge "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_MSMSulc.native.shape.gii -metric "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_MSMSulc.native.shape.gii -column 2
${CARET7DIR}/wb_command -metric-math "ln(var) / ln (2)" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_MSMSulc.native.shape.gii -var var "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_MSMSulc.native.shape.gii
${CARET7DIR}/wb_command -metric-math "ln(var) / ln (2)" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_MSMSulc.native.shape.gii -var var "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_MSMSulc.native.shape.gii
rm "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_MSMSulc.native.shape.gii

RegSphere="${AtlasSpaceFolder}/${NativeFolder}/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii"

./global/scripts/MSMSulc.sh
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RegSphere="${AtlasSpaceFolder}/${NativeFolder}/${Subject}.${Hemisphere}.sphere."$RegName".native.surf.gii"
else
RegSphere="${AtlasSpaceFolder}/${NativeFolder}/${Subject}.${Hemisphere}.sphere.reg.reg_LR.native.surf.gii"
fi
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117 changes: 117 additions & 0 deletions global/scripts/MSMSulc.sh
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@@ -0,0 +1,117 @@
#!/bin/bash
set -eu

pipedirguessed=0
if [[ ""$HCPPIPEDIR:-"" == "" ]]
then
pipedirguessed=1
#fix this if the script is more than one level below HCPPIPEDIR
export HCPPIPEDIR="$(dirname -- "$0")/.."
fi

source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"

#description of script/command
opts_SetScriptDescription "Run MSMSulc registration and save distortion outputs"

opts_AddMandatory '--subject-dir' 'SubjectDir' 'path' "folder containing all subjects"
opts_AddMandatory '--subject' 'Subject' 'subject ID' "subject-id"
opts_AddOptional '--regname' 'RegName' 'my reg' "set a new registration name, default MSMSulc" 'MSMSulc'
opts_AddOptional '--msm-conf' 'ConfFile' 'conf file' "provide the name of the configuration file, default MSMSulcStrainFinalconf" "$MSMCONFIGDIR"/MSMSulcStrainFinalconf
opts_AddOptional '--refmesh' 'RefMesh' 'ref mesh' "provide alternate standard sphere, default 164k_fs_LR, use .HEMISPHERE. instead of .L. or .R."
opts_AddOptional '--refdata' 'RefData' 'ref data' "provide alternate reference data, use .HEMISPHERE. instead of .L. or .R."

opts_ParseArguments "$@"

if ((pipedirguessed))
then
log_Err_Abort "HCPPIPEDIR is not set, you must first source your edited copy of Examples/Scripts/SetUpHCPPipeline.sh"
fi

#display the parsed/default values
opts_ShowValues

#set paths
SurfaceTemplateFolder="$HCPPIPEDIR"/global/templates/standard_mesh_atlases
NonlinearFolder="$SubjectDir"/"$Subject"/MNINonLinear
NativeFolder="$NonlinearFolder"/Native

#if user provided --refmesh but not --refdata, scream
if [[ "$RefMesh" != "" && "$RefData" == "" ]]
then
log_Err_Abort "Non-default standard sphere provided, but no non-default reference data"
fi

if [[ "$RefMesh" == "" ]]
then
RefMesh="$SurfaceTemplateFolder"/fsaverage.HEMISPHERE_LR.spherical_std.164k_fs_LR.surf.gii
fi

if [[ "$RefData" == "" ]]
then
RefData="$SurfaceTemplateFolder"/HEMISPHERE.refsulc.164k_fs_LR.shape.gii
fi

#do the same with the conf file
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#Make MSMSulc Directory
mkdir -p "$NativeFolder"/"$RegName"

#Loop through left and right hemispheres
for Hemisphere in L R ; do

if [[ "$Hemisphere" == "L" ]] ; then
Structure="CORTEX_LEFT"
elif [[ "$Hemisphere" == "R" ]] ; then
Structure="CORTEX_RIGHT"
fi
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#convert relative to absolute for correctness after cd, restrict HEMISPHERE replacement to filename only
RefMeshFile=$(basename -- "$RefMesh")
ReferenceMesh="$(cd "$(dirname -- "$RefMesh")"; pwd)/${RefMeshFile/HEMISPHERE/$Hemisphere}"
RefDataFile=$(basename -- "$RefData")
ReferenceData="$(cd "$(dirname -- "$RefData")"; pwd)/${RefDataFile/HEMISPHERE/$Hemisphere}"
(
cd "$NativeFolder"/"$RegName"

#Register using FreeSurfer Sulc Folding Map Using MSM Algorithm Configured for Reduced Distortion
"$MSMBINDIR"/msm --conf="$ConfFile" --inmesh="$NativeFolder"/"$Subject"."$Hemisphere".sphere.rot.native.surf.gii --refmesh="$ReferenceMesh" --indata="$NativeFolder"/"$Subject"."$Hemisphere".sulc.native.shape.gii --refdata="$ReferenceData" --out="$NativeFolder"/"$RegName"/"$Hemisphere". --verbose
)

cp "$ConfFile" "$NativeFolder"/"$RegName"/"$Hemisphere".logdir/conf
cp "$NativeFolder"/"$RegName"/"$Hemisphere".sphere.reg.surf.gii "$NativeFolder"/"$Subject"."$Hemisphere".sphere."$RegName".native.surf.gii

wb_command -set-structure "$NativeFolder"/"$Subject"."$Hemisphere".sphere."$RegName".native.surf.gii "$Structure"

wb_command -surface-distortion "$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$NativeFolder"/"$Subject"."$Hemisphere".sphere."$RegName".native.surf.gii "$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_"$RegName".native.shape.gii
wb_command -set-map-names "$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_"$RegName".native.shape.gii -map 1 "$Subject"_"$Hemisphere"_Areal_Distortion_"$RegName"
wb_command -metric-palette "$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_"$RegName".native.shape.gii MODE_AUTO_SCALE -palette-name ROY-BIG-BL -thresholding THRESHOLD_TYPE_NORMAL THRESHOLD_TEST_SHOW_OUTSIDE -1 1

wb_command -surface-distortion "$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$NativeFolder"/"$Subject"."$Hemisphere".sphere."$RegName".native.surf.gii "$NativeFolder"/"$Subject"."$Hemisphere".EdgeDistortion_"$RegName".native.shape.gii -edge-method
wb_command -surface-distortion "$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$NativeFolder"/"$Subject"."$Hemisphere".sphere."$RegName".native.surf.gii "$NativeFolder"/"$Subject"."$Hemisphere".Strain_"$RegName".native.shape.gii -local-affine-method -log2

wb_command -metric-merge "$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_"$RegName".native.shape.gii -metric "$NativeFolder"/"$Subject"."$Hemisphere".Strain_"$RegName".native.shape.gii -column 1
wb_command -metric-merge "$NativeFolder"/"$Subject"."$Hemisphere".StrainR_"$RegName".native.shape.gii -metric "$NativeFolder"/"$Subject"."$Hemisphere".Strain_"$RegName".native.shape.gii -column 2

rm "$NativeFolder"/"$Subject"."$Hemisphere".Strain_"$RegName".native.shape.gii
done

#Create CIFTI Files
wb_command -cifti-create-dense-scalar "$NativeFolder"/"$Subject".ArealDistortion_"$RegName".native.dscalar.nii -left-metric "$NativeFolder"/"$Subject".L.ArealDistortion_"$RegName".native.shape.gii -right-metric "$NativeFolder"/"$Subject".R.ArealDistortion_"$RegName".native.shape.gii
wb_command -set-map-names "$NativeFolder"/"$Subject".ArealDistortion_"$RegName".native.dscalar.nii -map 1 "$Subject"_ArealDistortion_"$RegName"
wb_command -cifti-palette "$NativeFolder"/"$Subject".ArealDistortion_"$RegName".native.dscalar.nii MODE_USER_SCALE "$NativeFolder"/"$Subject".ArealDistortion_"$RegName".native.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

wb_command -cifti-create-dense-scalar "$NativeFolder"/"$Subject".EdgeDistortion_"$RegName".native.dscalar.nii -left-metric "$NativeFolder"/"$Subject".L.EdgeDistortion_"$RegName".native.shape.gii -right-metric "$NativeFolder"/"$Subject".R.EdgeDistortion_"$RegName".native.shape.gii
wb_command -set-map-names "$NativeFolder"/"$Subject".EdgeDistortion_"$RegName".native.dscalar.nii -map 1 "$Subject"_EdgeDistortion_"$RegName"
wb_command -cifti-palette "$NativeFolder"/"$Subject".EdgeDistortion_"$RegName".native.dscalar.nii MODE_USER_SCALE "$NativeFolder"/"$Subject".EdgeDistortion_"$RegName".native.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

wb_command -cifti-create-dense-scalar "$NativeFolder"/"$Subject".StrainJ_"$RegName".native.dscalar.nii -left-metric "$NativeFolder"/"$Subject".L.StrainJ_"$RegName".native.shape.gii -right-metric "$NativeFolder"/"$Subject".R.StrainJ_"$RegName".native.shape.gii
wb_command -set-map-names "$NativeFolder"/"$Subject".StrainJ_"$RegName".native.dscalar.nii -map 1 "$Subject"_StrainJ_"$RegName"
wb_command -cifti-palette "$NativeFolder"/"$Subject".StrainJ_"$RegName".native.dscalar.nii MODE_USER_SCALE "$NativeFolder"/"$Subject".StrainJ_"$RegName".native.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

wb_command -cifti-create-dense-scalar "$NativeFolder"/"$Subject".StrainR_"$RegName".native.dscalar.nii -left-metric "$NativeFolder"/"$Subject".L.StrainR_"$RegName".native.shape.gii -right-metric "$NativeFolder"/"$Subject".R.StrainR_"$RegName".native.shape.gii
wb_command -set-map-names "$NativeFolder"/"$Subject".StrainR_"$RegName".native.dscalar.nii -map 1 "$Subject"_StrainR_"$RegName"
wb_command -cifti-palette "$NativeFolder"/"$Subject".StrainR_"$RegName".native.dscalar.nii MODE_USER_SCALE "$NativeFolder"/"$Subject".StrainR_"$RegName".native.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

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