Usage

There are three primary inputs to the hbcd_qmri_postproc tool. In each case, the input is provided as a “study-wide” folder, such that the tool can be run on multiple subjects at once. These three directories include the BIDS directory, the relaxometry maps directory, and the segmentations directory.

At the time this application is run, there should be subject (and session, if desired) specific folders for each subject you want to process. Processing will iterate through each subject in the BIDS directory, find associated sessions with the relevant data, and create the necessary folders and files in the output directory. Processing is totally independent across subjects and sessions, so that the results will be the same if the subjects are processed in parallel or through a single call of this application.

The design of the application is meant to follow general BIDS-App guidelines. For more details on general usage principles of BIDS-Apps, see the linked documentation.

As described in the installation section, this tool is meant to be interacted with in containerized form. The example below shows the general layout for how you may want to interact with the container to conduct processing if you have the container downloaded as a singularity image:

container_path=/path/to/container.sif
bids_dir=/path/to/bids
output_dir=/path/to/output
qmri_dir=/path/to/qmri
bibsnet_dir=/path/to/bibsnet

singularity run -B $bids_dir:/bids \
      -B $output_dir:/output \
      -B $qmri_dir:/qmri \
      -B $bibsnet_dir:/bibsnet \
      $container_path /data /output participant /qmri /bibsnet

To see more specific information about how this tool expects the inputs to be formatted (i.e. file naming conventions), see the inputs formatting page.

Command-Line Arguments

usage: hbcd_qmri_postproc [-h] [--participant_label PARTICIPANT_LABEL]
                          [--session_id SESSION_ID] [--overwrite_existing]
                          [--skip_existing]
                          [--region_groupings_json REGION_GROUPINGS_JSON [REGION_GROUPINGS_JSON ...]]
                          [--sequence_name_source SEQUENCE_NAME_SOURCE]
                          bids_dir output_dir analysis_level qmri_deriv_dir
                          bibsnet_deriv_dir

Positional Arguments

bids_dir: The path to the BIDS directory for your study (this is the same for all subjects)
output_dir: The path to the folder where outputs will be stored (this is the same for all subjects)
analysis_level: Should always be participant
qmri_deriv_dir: The path to the folder where the qMRI Relaxometry Maps are stored (this is the same for all subjects)
bibsnet_deriv_dir: The path to the folder where the BIBSNET/CABINET segmentations are stored (this is the same for all subjects)

Named Arguments

--participant_label, --participant-label: The name/label of the subject to be processed (i.e. sub-01 or 01)
--session_id, --session-id: OPTIONAL: the name of a specific session to be processed (i.e. ses-01)
--overwrite_existing: OPTIONAL: if flag is activated, the tool will delete the session folder where outputs are to be stored before processing if said folder already exists.
--skip_existing: OPTIONAL: if flag is activated, the tool will skip processing for a session if the session folder where outputs are to be stored already exists.
--region_groupings_json: OPTIONAL: the path to a json file containing region groupings for which to calculate statistics. Multiple files can be provided, resulting in multiple output csv files.
--sequence_name_source: OPTIONAL: the the key for the key/value pair to try and grab sequence name from. For example if the qMRI file is named sub-1_acq-QALAS.nii.gz, this should be “acq”. If the sequence is found, it will be represented as “quant” in the output files.