tools/batch_run_defacing_script.pl

[cmadjar]

Test plan

• [x] Determine which modalities to deface (Usually, all anatomical scans T1W, FLAIR, T2W, T2 star, MP2RAGE, fieldmap magnitude…)

• [x] Set up the following settings in the Config module under the “Imaging Pipeline” section:

• “Scan type to use as a reference for defacing...”: select the T1W scan type

• “Modalities on which to run the defacing pipeline”: select the modalities to deface

• [ ] ~Ensure QSUB is installed and setup on the VM~ QSUB not longer available on ubuntu

• [ ] ~Ensure the config setting “Project batch management used” is set to “Yes”~ QSUB no longer available on ubuntu

• [x] Create a text file with the list of session IDs to process (one session ID per line)

• [x] Run the following command using the list of session IDs created in a. (sessionIDs_list)

  batch_run_defacing_script.pl -profile prod < sessionIDs_list

• [x] Check sessionIDs were defaced:

  SELECT COUNT(*) FROM files f JOIN mri_scan_type mst ON (f.AcquisitionProtocolID=mst.ID) WHERE Scan_type='t1';
  SELECT COUNT(*) FROM files f JOIN mri_scan_type mst ON (f.AcquisitionProtocolID=mst.ID) WHERE Scan_type='t1-defaced';