# Docker / Apptainer

## Docker

### Get image from docker hub

```bash
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:

```bash
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](https://hub.docker.com/repository/docker/cpplab/bidspm)
and start the docker image::

```bash
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`):

```bash
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.

```bash
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](https://apptainer.org/) (formerly Singularity) to run bidspm,
a definition file is provided in the repository.

```bash
apptainer build bidspm.sif bidspm.def
```