Adding the preprocessing code back #81
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Fixes #80. Adds the removed code back to
preprocess_segment.sh.Steps to reproduce this PR:
Data:
duke/temp/rohan/bids_dataConfig file values:
{ "path_data": "PATH_TO_BIDS_DATA", "include-list": "sub-HarshmanDobby", "data_type": "anat", "contrast": "t2", "suffix_image": "_T2", "first_disc": "1", "last_disc": "26" }Run the
preprocess_segment.shusing thesct_run_batchfrom theREADMEof this PR.Expected output
Running this script should create a temporary output folder with the
segmentationanddisc_levelderivatives with the names:{SUBJECT_NAME_CONTRAST}_label-SC_mask.nii.gz
{SUBJECT_NAME_CONTRAST}_labeled-discs.nii.gz