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