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BUG: Fix precision issues causing priors to get zeroed out #1197

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Jun 15, 2021
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BUG: Fix precision issues causing priors to get zeroed out #1197

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6 changes: 4 additions & 2 deletions Scripts/antsCookTemplatePriors.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -605,15 +605,17 @@ if [[ ${TEMPLATE_PRIORS_EXIST} -eq 0 ]];
TMP_CSF_POSTERIOR=${OUTPUT_PREFIX}BrainSegmentationCsfPosteriorTmp.${OUTPUT_SUFFIX}
logCmd ${ANTSPATH}/SmoothImage ${DIMENSION} ${TEMPLATE_POSTERIORS[0]} 1 ${TMP_CSF_POSTERIOR} 1
logCmd ${ANTSPATH}/ImageMath ${DIMENSION} ${TEMPLATE_PRIORS[0]} max ${TEMPLATE_PRIORS[0]} ${TMP_CSF_POSTERIOR}
# Clip priors to remove precision errors
logCmd ${ANTSPATH}/ImageMath ${DIMENSION} ${TEMPLATE_PRIORS[0]} WindowImage ${TEMPLATE_PRIORS[0]} 0 1 0 1

# Brian's finishing touches on "cooking"---subtract out CSF from all other priors
for (( j = 1; j < ${#TEMPLATE_PRIORS[@]}; j++ ))
do
let PRIOR_LABEL=$j+1

logCmd ${ANTSPATH}/ImageMath ${DIMENSION} ${TEMPLATE_PRIORS[$j]} - ${TEMPLATE_PRIORS[$j]} ${TEMPLATE_PRIORS[0]}
logCmd ${ANTSPATH}/ThresholdImage ${DIMENSION} ${TEMPLATE_PRIORS[$j]} ${TMP_CSF_POSTERIOR} 0 1 1 0
logCmd ${ANTSPATH}/ImageMath ${DIMENSION} ${TEMPLATE_PRIORS[$j]} m ${TEMPLATE_PRIORS[$j]} ${TMP_CSF_POSTERIOR}
# Clip priors to range [0,1]
logCmd ${ANTSPATH}/ImageMath ${DIMENSION} ${TEMPLATE_PRIORS[$j]} WindowImage ${TEMPLATE_PRIORS[$j]} 0 1 0 1
done

logCmd rm -f $TMP_CSF_POSTERIOR
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