Try It

Run SpinalfMRIprep on sample data in under 5 minutes.

Prerequisites

• Docker Desktop (or Apptainer/Singularity)
• 10 GB free disk space

One-Command Install

# Clone and install
git clone https://github.com/SpinalfMRIprep/SpinalfMRIprep.git
cd SpinalfMRIprep
pip install poetry && poetry install

Download Sample Data

SpinalfMRIprep provides a script to download a minimal test dataset from OpenNeuro:

# Download 1 subject from ds005884 (Motor task)
poetry run spinalfmriprep download-sample --dataset ds005884 --subjects 1

This downloads ~500 MB of data to data/ds005884/.

Pull Container Images

docker pull vnmd/spinalcordtoolbox_7.2:20251215

Run Preprocessing

# Run all steps on the sample data
poetry run spinalfmriprep run all \
  --bids-root data/ds005884 \
  --out work/tryit

View Results

Open the QC dashboard in your browser:

open work/tryit/derivatives/spinalfmriprep/qc_dashboard.html

You should see: - ✅ S0 Setup: PASS - ✅ S1 Input Verify: PASS
- ✅ S2 Anat Cord Ref: PASS - ✅ S3 Func Init: PASS

Next Steps