Project Setup

Overview

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 option.

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

Command

clpipe project_setup

Initialize a clpipe project.

clpipe project_setup [OPTIONS]

Options

-project_title <project_title>

Choose a title for your project.

-project_dir <project_dir>

Required Where the project will be located.

-source_data <source_data>

Where the raw data (usually DICOMs) are located.

-move_source_data

Move source data into project/data_DICOMs folder. USE WITH CAUTION.

-symlink_source_data

Symlink the source data into project/data_dicoms. Usually safe to do.

-profile <profile>

The batch profile you would like to use. Default is unc. The options include: “unc”, “duke”, “uva”, “pitt”

-debug

Flag to enable detailed error messages and traceback.