Skip to content

De-identifying NIfTI Headers

Shared with the CNT

This procedure runs on infrastructure the lab and the CNT operate together. The CNT manual keeps its own copy; changes to the shared steps are agreed with the CNT.

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).

This procedure de-identifies NIfTI images on cnt1 with the deid_json script.

To use this script, the images must be in NIfTI format. To convert from DICOM to NIfTI, use this sop.

  1. On cnt1, de-identify the NIfTI images using deid_json.
    1. In MobaXterm, on cnt1, go to /project/imaging_process/programs/deid_json/ and open the deid_json_queue.txt file.
    2. On each line, type /mnt/cnt-fs/imaging_process_fs/imaging_bids/subRIDXXX, then save.
      1. Press Enter so that there is an empty line below the last entry.
    3. Go to /project/imaging_process/programs/heudiconv_3T/.
    4. Type bash deid_json.sh and press Enter to run it.