tsconcat

BIDS App and Python library for concatenating MRI time series.

Inspired by Cho et al. 2021.

Features

• Concatenate BOLD time series from multiple datasets, sessions, subjects or runs into a single file.
• Dry run mode to check what the output directory will look like.
• Fake mode to produce a bids2table compatible parquet output directory.

Installation

Get the newest development version via:

pip install git+https://github.com/childmindresearch/tsconcat

Quick start

ba-tsconcat /path/to/input/bids /path/to/output group --concat ses --dry_run

Usage

ba-tsconcat --help
usage: ba-tsconcat [-h] [-c CONCAT] [-d] [-f] bids_dir output_dir {group}

Concatenate MRI timeseries.

positional arguments:
  bids_dir              Input BIDS folder path.
  output_dir            Output BIDS folder path.
  {group}               Processing stage, must be "group".

options:
  -h, --help            show this help message and exit
  -c CONCAT, --concat CONCAT
                        Concat across. Can be any combination of dataset, sub, ses, run separated by spaces. Output data will be grouped by the set difference.
  -d, --dry_run         Dry run. Print output directory structure instead of actually doing something. If this is enabled 'bids_dir' may be a path to a bids2table parquet directory.
  -f, --fake            Fake output. Output a bids2table parquet directory instead of actually doing something.

Links or References

• Impact of concatenating fMRI data on reliability for functional connectomics (Cho et al. 2021)
• bids2table