code/compare_deid.py: get stats on gray matter alone

proj-nuisance / nuisance

Explaining human MRI data using phantom data QA metrics

Apache License 2.0

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Open yarikoptic opened 3 years ago

yarikoptic commented 3 years ago

make sure that it is the ..._acq-MPRAGE_T1w_reoriented_brain_seg.nii.gz which contains the final segmentation of gray/white/csf. (and not _pveseg.nii.gz). Sample directory /home/chrispycheng/proj/nuisance/data/dbic/simple_workflow/sub-sid000278_ses-20170307X152148_acq-MPRAGE_T1w/segs
adjust the script so it takes only gray matter voxels (almost there)

chrispycheng commented 3 years ago

Complete, the files are in output/deid-effects in nuisance on smaug