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De-identifying NIfTI Headers

What this page tells you

De-identify nifti images in cnt1: add each /mnt/cnt-fs/imaging_process_fs/imaging_bids/subRIDXXX path to deid_json_queue.txt in /project/imaging_process/programs/deid_json (blank trailing line), then run bash deid_json.sh from the heudiconv_3T folder. Images must be nifti first (see dicom-to-nifti page).

KNOWLEDGE BASE (a page (retired page))

  • to use this script, images must be in nifti format

  • use this sop to convert from dicom to nifti

  • in cnt1 de-identify the nifti images using deid_json

    1. in MobaXterm, in cnt1 go to: /project/imaging_process/programs/deid_json/, open the deid_json_queue.txt file
    2. for each line, type /mnt/cnt-fs/imaging_process_fs/imaging_bids/subRIDXXX, then hit save
      1. hit enter so there is an empty line below the script
    3. go to /project/imaging_process/programs/heudiconv_3T/ (Mariam needs to update path)
    4. type bash deid_json.sh and hit enter to run