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check-missing-processing - Check missing processing in a CAPS directory

Starting from a CAPS compliant dataset, this command creates a TSV file with columns participant_id, session_id and names corresponding to steps of t1-volume, t1-freesurfer, t1-linear, pet-volume and pet-surface.

For PET pipelines one column is created per tracer and the PVC option is considered for pet-volume.

clinica iotools check-missing-processing BIDS_DIRECTORY CAPS_DIRECTORY OUTPUT_FILE

where:

  • BIDS_DIRECTORY: input folder of a BIDS compliant dataset
  • CAPS_DIRECTORY: input folder of a CAPS compliant dataset
  • OUTPUT_FILE: output file path (filename included).

The content of output_file will look like:

participant_id   session_id     t1-linear   ...     pet-volume_trc-<tracer>_group-<group_label>_pvc-{True|False}
sub-01           ses-M000        1                   1
sub-01           ses-M012        1                   0
sub-02           ses-M000        0                   0
  • columns associated with pet-volume outputs will specify the PET tracer, the group label and if a PVC correction was performed.
  • columns associated with t1-volume outputs will specify the group label and which steps of t1-volume were performed.
  • columns associated with pet-surface outputs will specify the PET tracer used.

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