⚙️ How to use cwas-rsfmri?

BIDS-App principle¶

This pipeline follows the BIDS-App workflow. This means, it takes connectome files in BIDS-fortmat (BEP-017) as an input.

In one simple command line, the wokflow will be launched.

Example usage¶

cwas-rsfmri --bids_dir=bids_directory --output_dir=results --atlas_file=atlas.txt --atlas=example_atlas --phenotype_file=participants.tsv --group=diagnosis --case_id=NDD --control_id=HC --session=timepoint1 --task=task01 --run=01 --feature=denoiseSimple

Options¶

Paths¶

--bids_dir : BIDS directory where all the connectomes are located

--output_dir : Directory to save results. This folder will be automatically created

--atlas_file: Path to atlas description file (.txt or .tsv accepted)

--phenotype_file: Indicate the location of your phenotype file. Accepted extension file: .tsv .csv or .xlsx

File selection¶

CWAS-rsfmri expect BIDS-formatted connectomes (following BEP-017). For more information, please see the BEP-017 proposal.

To select specific task, run and atlas, please refer to your filename: sub-{}_ses-{}_task-{}_run-{}_seg-{atlas}_desc-{feature}_relmat_.tsv

--atlas: The name of your atlas as indicated in your filename.

--feature: Description of the feature used for the denoising pipeline.

--session: Session to process.

--task: Task to process.

--run: Run to process.

Phenotype information¶

Required columns are indicated in bold, optional in italic.

From your phenotype file you can indicate the following flags:

--group: Group comparison to perform (e.g. diagnosis). Indicate the column name.

--case_id: Indicate the variable name of your case groupe (e.g. SCHZ).

--control_id: Indicate the variable name of your control groupe (e.g. HC).

Optional

--scanner: Indicate True if you have different scanner settings. Default to False.

--sequence: Indicate True if you have different sequence settings. Default to False.

--medication: Indicate True if you have medication indications. Default to False.