Try a demo

Brainana ships with a small, ready-to-run BIDS dataset — one macaque subject with two T1w runs, one T2w, and two resting-state fMRI runs — so you can exercise the full pipeline (including multi-run anatomical selection) end to end.

Download just the demo dataset from the project repository:

git clone --depth 1 --filter=blob:none --sparse https://github.com/xingyu-liu/brainana.git
cd brainana
git sparse-checkout set examples/dataset_example

This needs git ≥ 2.25; on older git, clone the whole repository instead with git clone https://github.com/xingyu-liu/brainana.git.

Run it

From the repository root, point Brainana at examples/dataset_example as the input:

docker run -it --rm --gpus all \
    -v "$(pwd)/examples/dataset_example":/input \
    -v <path/to/output_dir>:/output \
    -v <path/to/work_dir>:/output_wd \
    -v <path/to/license.txt>:/fs_license.txt \
    liuxingyu987/brainana:<version> /input /output \
    --work_dir /output_wd --freesurfer_license /fs_license.txt

Replace <version> with a published tag (e.g. 2.0.0), and create the output and work directories beforehand so results are owned by you, not root (see I don’t want Brainana to run as root. I want it to run as my own user. What should I do?). Running without a GPU or without a FreeSurfer license is covered in the Docker user guide.

Expected result

The full run finishes in about 20 minutes with the GPU on a typical workstation (8 CPU cores, 20 GB RAM, one NVIDIA GPU); CPU-only is roughly 60% slower. Outputs follow the BIDS-derivatives layout in Outputs, with a browsable HTML QC report (sub-example.html) at the output root — see a sample report.