*Don't mix reference space between T1w and MNINonLinear files to enab…

…le T1w to have a different space from MNI152 in certain cases (e.g., direct import from FreeSurfer recon-all without running all of PreFreeSurfer).
Washington-University · Mar 20, 2023 · 655e69b · 655e69b
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commit 655e69b
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diff --git a/PostFreeSurfer/scripts/CreateMyelinMaps.sh b/PostFreeSurfer/scripts/CreateMyelinMaps.sh
@@ -143,18 +143,18 @@ if [ "${T2wPresent}" = "YES" ] ; then
 fi
 
 # Do the same for the equivalents in MNINonLinear space
-convertwarp --relout --rel --ref="$T1wImageBrainMask" --warp1="$OutputOrigT1wToT1w" --warp2="$AtlasTransform" --out="$OutputOrigT1wToStandard"
-applywarp --rel --interp=spline -i "$BiasField" -r "$T1wImageBrainMask" -w "$AtlasTransform" -o "$BiasFieldOutput"
+convertwarp --relout --rel --ref="$OutputMNIT1wImage" --warp1="$OutputOrigT1wToT1w" --warp2="$AtlasTransform" --out="$OutputOrigT1wToStandard"
+applywarp --rel --interp=spline -i "$BiasField" -r "$OutputMNIT1wImage" -w "$AtlasTransform" -o "$BiasFieldOutput"
 fslmaths "$BiasFieldOutput" -thr 0.1 "$BiasFieldOutput"
 
-applywarp --rel --interp=spline -i "$OrginalT1wImage" -r "$T1wImageBrainMask" -w "$OutputOrigT1wToStandard" -o "$OutputMNIT1wImage"
+applywarp --rel --interp=spline -i "$OrginalT1wImage" -r "$OutputMNIT1wImage" -w "$OutputOrigT1wToStandard" -o "$OutputMNIT1wImage"
 fslmaths "$OutputMNIT1wImage" -abs "$OutputMNIT1wImage" -odt float
 fslmaths "$OutputMNIT1wImage" -div "$BiasFieldOutput" "$OutputMNIT1wImageRestore"
 fslmaths "$OutputMNIT1wImageRestore" -mas "$T1wMNIImageBrainMask" "$OutputMNIT1wImageRestoreBrain"
 
 if [ "${T2wPresent}" = "YES" ] ; then
-  convertwarp --relout --rel --ref="$T1wImageBrainMask" --warp1="$OutputOrigT2wToT1w" --warp2="$AtlasTransform" --out="$OutputOrigT2wToStandard"
-  applywarp --rel --interp=spline -i "$OrginalT2wImage" -r "$T1wImageBrainMask" -w "$OutputOrigT2wToStandard" -o "$OutputMNIT2wImage"
+  convertwarp --relout --rel --ref="$OutputMNIT1wImage" --warp1="$OutputOrigT2wToT1w" --warp2="$AtlasTransform" --out="$OutputOrigT2wToStandard"
+  applywarp --rel --interp=spline -i "$OrginalT2wImage" -r "$OutputMNIT1wImage" -w "$OutputOrigT2wToStandard" -o "$OutputMNIT2wImage"
   fslmaths "$OutputMNIT2wImage" -abs "$OutputMNIT2wImage" -odt float
   fslmaths "$OutputMNIT2wImage" -div "$BiasFieldOutput" "$OutputMNIT2wImageRestore"
   fslmaths "$OutputMNIT2wImageRestore" -mas "$T1wMNIImageBrainMask" "$OutputMNIT2wImageRestoreBrain"

diff --git a/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh b/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh
@@ -170,7 +170,7 @@ echo "0 0 0 1"          >> ${FreeSurferFolder}/mri/c_ras.mat
 for Image in wmparc aparc.a2009s+aseg aparc+aseg ; do
     if [ -e "$FreeSurferFolder"/mri/"$Image".mgz ] ; then
         mri_convert -rt nearest -rl "$T1wFolder"/"$T1wImage".nii.gz "$FreeSurferFolder"/mri/"$Image".mgz "$T1wFolder"/"$Image"_1mm.nii.gz
-        applywarp --rel --interp=nn -i "$T1wFolder"/"$Image"_1mm.nii.gz -r "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage" --premat=$FSLDIR/etc/flirtsch/ident.mat -o "$T1wFolder"/"$Image".nii.gz
+        applywarp --rel --interp=nn -i "$T1wFolder"/"$Image"_1mm.nii.gz -r "$T1wFolder"/"$T1wImage".nii.gz --premat=$FSLDIR/etc/flirtsch/ident.mat -o "$T1wFolder"/"$Image".nii.gz
         applywarp --rel --interp=nn -i "$T1wFolder"/"$Image"_1mm.nii.gz -r "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage" -w "$AtlasTransform" -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
@@ -181,7 +181,7 @@ done
 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"/"$AtlasSpaceT1wImage" --premat=$FSLDIR/etc/flirtsch/ident.mat -o "$T1wFolder"/"$T1wImageBrainMask".nii.gz
+applywarp --rel --interp=nn -i "$T1wFolder"/"$T1wImageBrainMask"_1mm.nii.gz -r "$T1wFolder"/"$T1wImage".nii.gz --premat=$FSLDIR/etc/flirtsch/ident.mat -o "$T1wFolder"/"$T1wImageBrainMask".nii.gz
 applywarp --rel --interp=nn -i "$T1wFolder"/"$T1wImageBrainMask"_1mm.nii.gz -r "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage" -w "$AtlasTransform" -o "$AtlasSpaceFolder"/"$T1wImageBrainMask".nii.gz
 
 #Add volume files to spec files