BIDS Validation

Overview

clpipe contains a convenience function to validate your datasets directly on the HPC. This function uses a Singularity image of the BIDs Validator.

The output of this command will appear in your logs/bids_validation_logs folder by default.

Notably, fMRIPrep will refuse to run non-valid BIDS datasets, unless you turn the option off. The same bids-validator outputs can be viewed in fMRIPrep’s logs, but you may find this stand-alone command more convenient.

Configuration

Definitions

class clpipe.config.options.BIDSValidatorOptions

Options for validating your BIDS directory.

bids_validator_image: str = '/proj/hng/singularity_imgs/validator.simg'

Path to your BIDS validator image.

Command

clpipe bids_validate

Validate if a directory BIDS standard.

Validates the directory at BIDS_DIR, or at the BIDS directory in your config file’s DICOMToBIDSOptions if -config_file is given.

Results are viewable in logs/bids_validation_logs unless -interactive is used.

clpipe bids_validate [OPTIONS] [BIDS_DIR]

Options

-config_file, -c <config_file>

Required The path to your clpipe configuration file.

-log_dir <log_dir>

Where to put your HPC output files (such as SLURM output files).

-verbose, -v

Creates verbose validator output. Use if you want to see ALL files with errors/warnings.

-submit, -s

Flag to submit commands to the HPC.

-interactive

Run in interactive mode. Only use in an interactive compute session.

-debug, -d

Flag to enable detailed error messages and traceback.

Arguments

BIDS_DIR

Optional argument