Skip to content

Pipelines Overview

Command to Run a Pipeline

cvdproc --config_file <path/to/your/config/file> --run_pipeline --pipeline <pipeline name> --subject_id <subject id (with out -sub prefix)> --session_id <session id (with out -ses prefix)>

Generally, parameters concerning the pipeline should be set in the configuration file (this configuration file has been mentioned in the dcm2bids section). As we already set the bids_dir parameter in the configuration file, we will need to add some new parameters: 

# For example
bids_dir: /mnt/f/BIDS/demo_wmh # we have done it in the dcm2bids section
dcm2bids: 
  config_file: /mnt/f/BIDS/demo_wmh/code/dcm2bids_config.json
# New things
output_dir: /mnt/f/BIDS/demo_wmh/derivatives # output directory, please use bids::/derivatives
pipelines:
    wmh_quantification: # the pipeline name, can be changed to any available pipeline (see below)
        # Then the pipeline-specific parameters go here
        use_which_flair: "acq-tra"
        use_which_t1w: 'acq-highres'
        seg_threshold: 0.5
        seg_method: "LST"
        location_method: ["Fazekas", "shiva", "McDonald"]
        ventmask_method: 'SynthSeg'
        use_bianca_mask: false
        normalize_to_mni: true
The --pipeline parameter is used to specify which pipeline to run. The --subject_id and --session_id parameters are used to specify the subject and session to be processed. You can run multiple subjects and sessions serially by specifying multiple --subject_id and --session_id parameters. For example, if you want to run the wmh_quantification pipeline for subjects SUB0001 and SUB0002, both at session 01, you can run: cvdproc --config_file /mnt/f/BIDS/demo_wmh/code/config.yml --run_pipeline --pipeline wmh_quantification --subject_id 0001 0002 --session_id 01 01.

The detailed parameters for each pipeline can be found in the respective documentation pages (see below). Parameters except for subject, session, and output_path should be set in the configuration file.

Currently Available Pipelines

Structural MRI (sMRI) Pipelines

Diffusion MRI (dMRI) Pipelines

Functional MRI (fMRI) Pipelines

  • fMRI Pipeline (fmri_pipeline)

Arterial Spin Labeling (ASL) Pipelines

  • ASL Pipeline (asl_pipeline)

Quantitative MRI (qMRI) Pipelines

  • QSM Pipeline (qsm_pipeline)
  • SEPIA QSM (deprecated, archived as a record of the processing used in our paper) (sepia_qsm)

DSC-MRI (PWI) Pipelines