3. Labels

ANTsPriors utilizes joint label fusion to get the DKT label set as defined on the 20 OASIS brains into the group template space. Labels are obtained according to the following steps:

1. Perform ANTs brain extraction on the group template. This prevents labels from jumping onto the skull.
2. Find atlas t1-weighted images, either with or without white matter labeled. Note that we have found using labeled images without white matter results in substantially better coverage of the gray matter labels.
3. Perform joint label fusion on the group template

antsJointLabelFusion.sh -d 3 -t ${OutDir}/${projectName}Template_template0.nii.gz \
  -o ${OutDir}/${projectName}Template_malf -c 2 -j 8 -k 1 \
  -x ${OutDir}/ExtraLongTemplate_BrainExtractionMask.nii.gz \
  -p ${OutDir}/malfPosteriors%04d.nii.gz ${atlaslabelcall}