BIDScycle

This project is a BIDS compatible tool for easy renaming of BIDS data.

Getting Started

To get started simply install using:

pip install bidscycle

or

pip install git+https://github.com/miltoncamacho/BIDScycle.git@main

for the bleading edge latest changes

Usage

usage: bidscycle [-h] {create-duplicates,switch-duplicate,clean-duplicates}

You will need to select from the different commands to perform:

create-duplicates

This command will help you create BIDS duplicates in any of the files that match the provided BIDS compatible filters.

usage: bidscycle create-duplicates [-h] -f entity=value[,value2] [--commit-msg COMMIT_MSG] [--dry-run] [--no-datalad] [-v] dataset

Argument	Description
dataset	Absolute path to the dataset containing sub-XX folders.
--filter,-f	Entity filter in the format entity=value[,value2].
--commit-msg	Optional commit message for saving the changes.
--dry-run	Perform a trial run without making any changes.
--no-datalad	Skip Datalad commands during execution.
-v	Enable verbose output for debugging purposes.

switch-duplicates

usage: bidscycle switch-duplicates [-h] -f entity=value[,value2] [--commit-msg COMMIT_MSG] [--dry-run] [--no-datalad] [-v] dataset

Argument	Description
dataset	Absolute path to the dataset containing sub-XX folders.
--filter,-f	Entity filter in the format entity=value[,value2] must contain dup.
--commit-msg	Optional commit message for saving the changes.
--dry-run	Perform a trial run without making any changes.
--no-datalad	Skip Datalad commands during execution.
-v	Enable verbose output for debugging purposes.

clean-duplicates

usage: bidscycle clean-duplicates [-h] [-f entity=value[,value2]] --keep_pattern N[,N2] [--commit-msg COMMIT_MSG] [--dry-run] [--no-datalad] [-v] dataset

Argument	Description
dataset	Absolute path to the dataset containing sub-XX folders.
--filter,-f	Entity filter in the format entity=value[,value2].
--keep_pattern	Pattern(s) to keep (comma‑separated; e.g., '__dup-01').
--commit-msg	Optional commit message for saving the changes.
--dry-run	Perform a trial run without making any changes.
--no-datalad	Skip Datalad commands during execution.
-v	Enable verbose output for debugging purposes.