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hsieh42 / exit_process

Exit process and project boards for tracking issues.
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DICOM anonymization codes and procedure #9

Closed hsieh42 closed 6 years ago

hsieh42 commented 6 years ago

Matlab version: https://sbia-svn/projects/CBIG-dicomAnonymization/dicomAnonymization/ New, lightweight and more flexible python code: /cbica/comp_space/CBIG/Scripts/Anonymization/dicom_manipulation-git/anonymization/remove_dicom_fields.py. The actual CBIG anonymization key (/cbica/comp_space/CBIG/Scripts/Anonymization/cbig_anonpattern.cfg) is encoded in the code above.

Lab members should be able to run the codes on their own to anonymize the DICOM files for the time being.

To anonymize DICOM files from any source,

  1. upload them to the cluster to /cbica/comp_space/CBIG/dropbox as yourself,
    1. you can upload them via mapped network drive, or
    2. you can use scp/winscp to upload them,
  2. wait about 1 hour for file ownership change from yourself to cbig,
  3. sudo login as cbig project user,
  4. move the data to /cbica/comp_space/CBIG/Data_phiSensitive,
  5. launch the anonymization code with remove_dicom_fields.py specified above and output the files to /cbica/projects/CBIG/Anonymized_to_Distribute/${receiver}, where receiver should be a cbica-cluster user.
  6. assign read permission to the $receiver using /cbica/comp_space/CBIG/Scripts/setPermission.sh. See https://github.com/hsieh42/exit_process/issues/41#issue-364258805

After the anonymization, another script /cbica/comp_space/CBIG/Scripts/setPermission.sh would be called to assign the read permission of the $output_dir to a specific user/project user. setPermission.sh has to be executed on a compute node through SGE submission and will not take effect if executed on an interactive node, i.e. crete, agora, etc.

hsieh42 commented 6 years ago

See #19. The github repo is created for python codes.

What about the original matlab codes and tomo anon code, also in matlab?

hsieh42 commented 6 years ago

Create another issue for tomo anon + decompress, see #27. Closing this thread.