dR2*

Usage

This repo provides a BIDS-app style pipeline (dR2star) for running on fMRIPrep derivatives. It scans each func/ directory, aggregates matching preprocessed BOLD runs, and writes one output per subject/session.

High-level flow:

• point to an fMRIPrep derivatives folder
• choose an output folder
• optionally limit participants/sessions

Example:

dR2star /path/to/fmriprep /path/to/output participant \
  --participant-label 01 02 \
  --ses-label V01 V02 V03

Output

Outputs are written under:

OUTPUT_DIR/sub-<label>/ses-<label>/anat/

Each session produces:

• sub-*_ses-*_space-MNI152NLin6Asym_res-2_desc-dR2star_dR2starmap.nii.gz
• a JSON sidecar with the same basename
• one or more censor files with matching basename

Container Details For Whoever is Maintaining This Repo

There are two github actions mechanisms that will result in a new Docker container being built. First, any changes to the "main" branch of the repository will result in a new version of the container with the tag "latest". At the time of writing, it takes less than 5 minutes for a new version of the container to appear following code updates.

The second mechanism is through a tagged release. To create a new tagged version of the container, publish a GitHub Release. The workflow will use the release tag as the container tag, stripping a leading "v" if present (for example, "v1.2.3" becomes "1.2.3"). The container is pushed to GitHub Container Registry (GHCR) at:

ghcr.io/larsen-lab/dr2star

In summary:

• push to main -> updates ghcr.io/larsen-lab/dr2star:latest
• publish a release -> publishes ghcr.io/larsen-lab/dr2star:

If you need to change the branch used for latest or add multi-arch builds, edit .github/workflows/docker-publish.yml.

Container Details For End Users

The container image is published to GitHub Container Registry (GHCR) as ghcr.io/larsen-lab/dr2star.

Docker pull:

docker pull ghcr.io/larsen-lab/dr2star:latest

Docker run:

docker run --rm \
  -v /path/to/fmriprep:/input_dir \
  -v /path/to/output:/output_dir \
  ghcr.io/larsen-lab/dr2star:latest \
  /input_dir /output_dir participant

Singularity/Apptainer pull:

apptainer pull dR2star.sif docker://ghcr.io/larsen-lab/dr2star:latest

Singularity/Apptainer run:

apptainer run --cleanenv \
  -B /path/to/fmriprep:/input_dir \
  -B /path/to/output:/output_dir \
  dR2star.sif \
  /input_dir /output_dir participant

Developing

See tests in t/. Run with make check

Provenance

Extracted from lncdtools on 2026-01-08.

git clone --branch dr2star-fmriprep --single-branch lncdtools dR2star
find -iname '*dR2star*' -not -ipath '*.git/*' |
  sed 's:^./:--path :'|
  xargs uv tool run git-filter-repo --force \
    --path Makefile \
    --path .github/workflows/ci.yml \