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
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