Address Mike's comments and multiple grayordinates resolutions

Address Mike's comments and make sure this works in the case of multiple grayordinates resolutions.

Author: glasserm

PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh

@@ -213,12 +213,15 @@ for GrayordinatesResolution in ${GrayordinatesResolutions} ; do
     ${CARET7DIR}/wb_command -volume-label-import "$AtlasSpaceFolder"/ROIs/wmparc."$GrayordinatesResolution".nii.gz ${SubcorticalGrayLabels} "$AtlasSpaceFolder"/ROIs/ROIs."$GrayordinatesResolution".nii.gz -discard-others
     [ "${T2wImage}" != "NONE" ] && 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"/"$AtlasSpaceT1wImage".nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage"."$GrayordinatesResolution".nii.gz
+    
+    #Run these to check segmentation
     applywarp --interp=nn -i "$AtlasSpaceFolder"/"$T1wImageBrainMask".nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/"$T1wImageBrainMask"."$GrayordinatesResolution".nii.gz
-    ${CARET7DIR}/wb_command -volume-math "(1-Brainmask)*CIFTIStandardSpace" "$AtlasSpaceFolder"/ROIs/MissingGrayordinates.nii.gz -var Brainmask "$AtlasSpaceFolder"/"$T1wImageBrainMask"."$GrayordinatesResolution".nii.gz -var CIFTIStandardSpace "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz
-    MissingGrayordinates=`fslstats "$AtlasSpaceFolder"/ROIs/MissingGrayordinates.nii.gz -V | awk '{print $1}'`
-    MissingBrainstem=`fslstats "$AtlasSpaceFolder"/ROIs/MissingGrayordinates.nii.gz -l 15.9 -u 16.1 -V | awk '{print $1}'`
-    echo "MissingGrayordinates,MissingBrainstem" > "$AtlasSpaceFolder"/ROIs/MissingGrayordinates.txt
-    echo "${MissingGrayordinates},${MissingBrainstem}" >> "$AtlasSpaceFolder"/ROIs/MissingGrayordinates.txt
+    ${CARET7DIR}/wb_command -volume-math "(!Brainmask)*CIFTIStandardSpace" "$AtlasSpaceFolder"/ROIs/MissingGrayordinates."$GrayordinatesResolution".nii.gz -var Brainmask "$AtlasSpaceFolder"/"$T1wImageBrainMask"."$GrayordinatesResolution".nii.gz -var CIFTIStandardSpace "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz
+    MissingGrayordinates=`fslstats "$AtlasSpaceFolder"/ROIs/MissingGrayordinates."$GrayordinatesResolution".nii.gz -V | awk '{print $1}'`
+    MissingBrainstem=`fslstats "$AtlasSpaceFolder"/ROIs/MissingGrayordinates."$GrayordinatesResolution".nii.gz -l 15.9 -u 16.1 -V | awk '{print $1}'`
+    echo "MissingGrayordinates,MissingBrainstem" > "$AtlasSpaceFolder"/ROIs/MissingGrayordinates."$GrayordinatesResolution".txt
+    echo "${MissingGrayordinates},${MissingBrainstem}" >> "$AtlasSpaceFolder"/ROIs/MissingGrayordinates."$GrayordinatesResolution".txt
+    #End run these
 done
 
 #Loop through left and right hemispheres

PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear_1res.sh

@@ -129,6 +129,15 @@ for GrayordinatesResolution in ${GrayordinatesResolutions} ; do
   ${CARET7DIR}/wb_command -volume-label-import "$AtlasSpaceFolder"/ROIs/wmparc."$GrayordinatesResolution".nii.gz ${SubcorticalGrayLabels} "$AtlasSpaceFolder"/ROIs/ROIs."$GrayordinatesResolution".nii.gz -discard-others
   [ "${T2wImage}" != "NONE" ] && 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"/"$AtlasSpaceT1wImage".nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage"."$GrayordinatesResolution".nii.gz
+  
+  #Run these to check segmentation
+  applywarp --interp=nn -i "$AtlasSpaceFolder"/"$T1wImageBrainMask".nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/"$T1wImageBrainMask"."$GrayordinatesResolution".nii.gz
+  ${CARET7DIR}/wb_command -volume-math "(!Brainmask)*CIFTIStandardSpace" "$AtlasSpaceFolder"/ROIs/MissingGrayordinates."$GrayordinatesResolution".nii.gz -var Brainmask "$AtlasSpaceFolder"/"$T1wImageBrainMask"."$GrayordinatesResolution".nii.gz -var CIFTIStandardSpace "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz
+  MissingGrayordinates=`fslstats "$AtlasSpaceFolder"/ROIs/MissingGrayordinates."$GrayordinatesResolution".nii.gz -V | awk '{print $1}'`
+  MissingBrainstem=`fslstats "$AtlasSpaceFolder"/ROIs/MissingGrayordinates."$GrayordinatesResolution".nii.gz -l 15.9 -u 16.1 -V | awk '{print $1}'`
+  echo "MissingGrayordinates,MissingBrainstem" > "$AtlasSpaceFolder"/ROIs/MissingGrayordinates."$GrayordinatesResolution".txt
+  echo "${MissingGrayordinates},${MissingBrainstem}" >> "$AtlasSpaceFolder"/ROIs/MissingGrayordinates."$GrayordinatesResolution".txt
+  #End run these
 done
 
 #Loop through left and right hemispheres