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:
.. code-block:: 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
):
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 \
--action 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 \
--action stats \
--preproc_dir /derivatives/bidspm-preproc \
--model_file /models/smdl.json \
--fwhm 8