Docker / Apptainer

Docker

Get image from docker hub

docker pull cpplab/bidspm:latest

Build the docker image locally

If you want to build the docker image locally and not pull it from the docker hub:

docker build . -f docker/Dockerfile -t cpplab/bidspm:latest

This will create an image with the tag name bidspm:latest.

Running make build_image will also build the stable version and a version tagged image.

Run the docker image

The following command would pull from our docker hub and start the docker image::

docker run -it --rm cpplab/bidspm:latest

The following command would do do the same, but it would also map 2 folders from your computer and run preprocessing on your dataset (assuming there is a task called auditory):

bids_dir=fullpath_to_bids_dataset
output_dir=fullpath_to_your_output_folder

docker run -it --rm \
    -v $bids_dir:/raw \
    -v $output_dir:/derivatives \
    cpplab/bidspm:latest \
        /raw \
        /derivatives \
        subject \
        --task auditory \
        preprocess \
        --fwhm 8

Similarly this would run the statistics provided you give a bids stats model file and the path to the preprocessed data.

bids_dir=fullpath_to_bids_dataset
output_dir=fullpath_to_your_output_folder
model=fullpath_to_your_bids_stats_model

docker run -it --rm \
    -v $bids_dir:/raw \
    -v $output_dir:/derivatives \
    -v $model:/models/smdl.json \
    cpplab/bidspm:latest \
        /raw \
        /derivatives \
        subject \
        stats \
        --preproc_dir /derivatives/bidspm-preproc \
        --model_file /models/smdl.json \
        --fwhm 8

Apptainer

If you are plaaning to use Apptainer (formerly Singularity) to run bidspm, a definition file is provided in the repository.

apptainer build bidspm.sif bidspm.def