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Extend the checking of the subcortical segmentation #165

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Feb 27, 2020
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Extend the checking of the subcortical segmentation #165

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Extend the checking of the subcortical segmentation to report separat…
mharms Feb 12, 2020
7cdc3e6
Add some subcortical missing/overlap counts after applying dilation, …
mharms Feb 18, 2020
5f81047
Keep the dilated version of the brainmask
mharms Feb 19, 2020
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81 changes: 74 additions & 7 deletions PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -214,14 +214,81 @@ for GrayordinatesResolution in ${GrayordinatesResolutions} ; do
[ "${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
### Report on subcortical segmentation (missing voxels and overlap with Atlas)

# Generate brain mask at appropriate resolution
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

# Compute subcortical grayordinates missing from the "Atlas" space (CIFTI standard space) based on the overall brain mask
MissingGrayordinates="$AtlasSpaceFolder"/ROIs/MissingGrayordinates."$GrayordinatesResolution"
${CARET7DIR}/wb_command -volume-math "(!Brainmask)*CIFTIStandardSpace" ${MissingGrayordinates}.nii.gz -var Brainmask "$AtlasSpaceFolder"/"$T1wImageBrainMask"."$GrayordinatesResolution".nii.gz -var CIFTIStandardSpace "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz
MissingGrayordinatesTotal=$(fslstats ${MissingGrayordinates}.nii.gz -V | awk '{print $1}')

# Repeat with brain mask dilated by 2 x GrayordinatesResolution
# Use -volume-dilate rather than 'fslmaths -dilF -dilF', for explicit control over the dilation distance
dilDist=$(echo "2 * $GrayordinatesResolution" | bc -l)
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Thinking about this, the expected nonoverlap doesn't really seem dependent on the voxel size, it depends more on how well the structurals are registered and segmented. If someone were to make a 4mm grayordinates space (because they hate being able to see any detail, presumably), this would dilate 8mm, while if resolution improves to 1.2mm, this would only dilate by 2.4mm.

Of course, in nonhuman subjects, the dilation distance would need to be scaled by brain size, and using the voxel resolution sort of does that.

Another option would be to actually measure the distance of all the non-overlap voxels from the ROI, and average them, but this would need a new wb_command implemented.

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I think it is okay because we are talking about specific standard grayordinates spaces.

${CARET7DIR}/wb_command -volume-dilate "$AtlasSpaceFolder"/"$T1wImageBrainMask"."$GrayordinatesResolution".nii.gz $dilDist NEAREST "$AtlasSpaceFolder"/"$T1wImageBrainMask"."$GrayordinatesResolution".dil2x.nii.gz
${CARET7DIR}/wb_command -volume-math "(!BrainmaskDil2x)*CIFTIStandardSpace" ${MissingGrayordinates}.dil2xBrainMask.nii.gz -var BrainmaskDil2x "$AtlasSpaceFolder"/"$T1wImageBrainMask"."$GrayordinatesResolution".dil2x.nii.gz -var CIFTIStandardSpace "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz
MissingGrayordinatesDil2xTotal=$(fslstats ${MissingGrayordinates}.dil2xBrainMask.nii.gz -V | awk '{print $1}')

# Split the Atlas and subject-specific ROIs into individual structures, so we can compute counts of missing voxels and overlap relative to specific structures
AtlasROIsSplit="$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".split
SubjROIsSplit="$AtlasSpaceFolder"/ROIs/ROIs."$GrayordinatesResolution".split
MissingSplit=${MissingGrayordinates}.split
${CARET7DIR}/wb_command -volume-all-labels-to-rois "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz 1 ${AtlasROIsSplit}.nii.gz
${CARET7DIR}/wb_command -volume-all-labels-to-rois "$AtlasSpaceFolder"/ROIs/ROIs."$GrayordinatesResolution".nii.gz 1 ${SubjROIsSplit}.nii.gz

# Create a version of subject-specific ROIs, dilated by 2 x GrayordinatesResolution
${CARET7DIR}/wb_command -volume-dilate ${SubjROIsSplit}.nii.gz $dilDist NEAREST ${SubjROIsSplit}.dil2x.nii.gz

# Volume with the *brainmask* voxels missing from the Atlas, with each structure as a separate frame
# (Note: need to binarize "Missing" to turn it into a mask, since it uses the original label values)
${CARET7DIR}/wb_command -volume-math "(Missing > 0) * Atlas" ${MissingSplit}.nii.gz -var Missing ${MissingGrayordinates}.nii.gz -repeat -var Atlas ${AtlasROIsSplit}.nii.gz

# Volume with the *brainmask* voxels after 2x dilation that are missing from the Atlas, with each structure as a separate frame
${CARET7DIR}/wb_command -volume-math "(MissingDil2x > 0) * Atlas" ${MissingSplit}.dil2xBrainMask.nii.gz -var MissingDil2x ${MissingGrayordinates}.dil2xBrainMask.nii.gz -repeat -var Atlas ${AtlasROIsSplit}.nii.gz

# Volume with the subject-specific subcortical labels that are *missing* from the corresponding Atlas label, with each structure as a separate frame
${CARET7DIR}/wb_command -volume-math "Atlas * (!Subj)" ${SubjROIsSplit}.missing.nii.gz -var Atlas ${AtlasROIsSplit}.nii.gz -var Subj ${SubjROIsSplit}.nii.gz

# Volume with the subject-specific subcortical labels after 2x dilation that *overlap* with the corresponding Atlas label, with each structure as a separate frame
${CARET7DIR}/wb_command -volume-math "(Atlas) * SubjDil2x" ${SubjROIsSplit}.dil2x.overlap.nii.gz -var Atlas ${AtlasROIsSplit}.nii.gz -var SubjDil2x ${SubjROIsSplit}.dil2x.nii.gz

# Volume with the subject-specific subcortical labels that *overlap* with the corresponding Atlas label, with each structure as a separate frame
${CARET7DIR}/wb_command -volume-math "(Atlas) * Subj" ${SubjROIsSplit}.overlap.nii.gz -var Atlas ${AtlasROIsSplit}.nii.gz -var Subj ${SubjROIsSplit}.nii.gz

# Volume with the subject-specific subcortical labels that are *outside* of the corresponding Atlas label, with each structure as a separate frame
${CARET7DIR}/wb_command -volume-math "(!Atlas) * Subj" ${SubjROIsSplit}.outside.nii.gz -var Atlas ${AtlasROIsSplit}.nii.gz -var Subj ${SubjROIsSplit}.nii.gz

# Extract summary counts
${CARET7DIR}/wb_command -volume-stats ${MissingSplit}.nii.gz -reduce SUM -show-map-name > ${MissingSplit}.stats.txt
${CARET7DIR}/wb_command -volume-stats ${MissingSplit}.dil2xBrainMask.nii.gz -reduce SUM -show-map-name > ${MissingSplit}.dil2xBrainMask.stats.txt
${CARET7DIR}/wb_command -volume-stats ${SubjROIsSplit}.missing.nii.gz -reduce SUM -show-map-name > ${SubjROIsSplit}.missing.stats.txt
${CARET7DIR}/wb_command -volume-stats ${SubjROIsSplit}.dil2x.overlap.nii.gz -reduce SUM -show-map-name > ${SubjROIsSplit}.dil2x.overlap.stats.txt
${CARET7DIR}/wb_command -volume-stats ${SubjROIsSplit}.overlap.nii.gz -reduce SUM -show-map-name > ${SubjROIsSplit}.overlap.stats.txt
${CARET7DIR}/wb_command -volume-stats ${SubjROIsSplit}.outside.nii.gz -reduce SUM -show-map-name > ${SubjROIsSplit}.outside.stats.txt

# Assemble output csv
# We assume in the following (without checking) that the structures from -volume-stats -show-map-name are consistent across all files
cut -d ':' -f 2 ${MissingSplit}.stats.txt > ${MissingSplit}.stats.roinames.txt
cut -d ':' -f 3 ${MissingSplit}.stats.txt > ${MissingSplit}.stats.value.txt
cut -d ':' -f 3 ${MissingSplit}.dil2xBrainMask.stats.txt > ${MissingSplit}.dil2xBrainMask.stats.value.txt
cut -d ':' -f 3 ${SubjROIsSplit}.missing.stats.txt > ${SubjROIsSplit}.missing.stats.value.txt
cut -d ':' -f 3 ${SubjROIsSplit}.dil2x.overlap.stats.txt > ${SubjROIsSplit}.dil2x.overlap.stats.value.txt
cut -d ':' -f 3 ${SubjROIsSplit}.overlap.stats.txt > ${SubjROIsSplit}.overlap.stats.value.txt
cut -d ':' -f 3 ${SubjROIsSplit}.outside.stats.txt > ${SubjROIsSplit}.outside.stats.value.txt

outFile="$AtlasSpaceFolder"/ROIs/MissingGrayordinates."$GrayordinatesResolution".txt
echo "Structure,nMissing2xDilBrainMaskFromAtlas,nMissingBrainMaskFromAtlas,nMissing2xDilROIFromAtlas,nMissingROIFromAtlas,nROIOverlapAtlas,nROIOutsideAtlas" > ${outFile}
echo "ALL,${MissingGrayordinatesDil2xTotal},${MissingGrayordinatesTotal},,,," >> ${outFile}
paste -d ',' ${MissingSplit}.stats.roinames.txt ${MissingSplit}.dil2xBrainMask.stats.value.txt ${MissingSplit}.stats.value.txt ${SubjROIsSplit}.missing.stats.value.txt ${SubjROIsSplit}.dil2x.overlap.stats.value.txt ${SubjROIsSplit}.overlap.stats.value.txt ${SubjROIsSplit}.outside.stats.value.txt | tr -d '[:blank:]' >> ${outFile}

# Cleanup
rm ${AtlasROIsSplit}* ${SubjROIsSplit}* ${MissingSplit}*
rm ${MissingGrayordinates}.dil2xBrainMask.nii.gz
#rm "$AtlasSpaceFolder"/"$T1wImageBrainMask"."$GrayordinatesResolution".dil2x.nii.gz

### End report on subcortical segmentation
done

#Loop through left and right hemispheres
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