Project Setup¶
clpipe contains a convenience command for setting up the directories and configuration files for a given neuroimaging project, in a way that makes it simple to change configuration options:
Usage: project_setup [OPTIONS]
Options:
-project_title TEXT [required]
-project_dir PATH Where the project will be located. [required]
-source_data DIRECTORY Where the raw data (usually DICOMs) are located.
-symlink_source_data symlink the source data into project/data_dicoms.
Usually safe to do.
-submit Flag to submit commands to the HPC
-debug Flag to enable detailed error messages and
traceback.
--help Show this message and exit.
This command will create the necessary directory structures, as well as create a default configuration file with many directory fields already filled out. For example,
|-- analyses
|-- clpipe_config.json
|-- conversion_config.json
|-- data_BIDS
| |-- CHANGES
| |-- code
| |-- dataset_description.json
| |-- derivatives
| |-- participants.json
| |-- participants.tsv
| |-- README
| |-- sourcedata
|-- data_DICOMs -> /symlink/to/your/dicoms
|-- data_fmriprep
|-- data_postproc
| |-- betaseries_default
| |-- betaseries_noGSR
| |-- betaseries_noScrub
| |-- postproc_default
| |-- postproc_noGSR
| |-- postproc_noScrub
|-- data_ROI_ts
| |-- postproc_default
|-- logs
| |-- betaseries_logs
| |-- DCM2BIDS_logs
| |-- postproc_logs
| |-- ROI_extraction_logs
|-- scripts