Brain Imaging Analysis Kit
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lcnature Fix gen design (#381)
* add a check in utils.gen_design so that when there is no event, an all-zero time series is directly generated

* add test for the changes

* add the example stimulus timing file of AFNI style

* remove the printing test line

* removed the conditional clause in generate_stimfunction of fmrisim.py, which shortens stim_function if its length is smaller than the product of total_time and temporal_resolution

* fix whitespace

* changed two `floor` to `round` in utils.gen_design, because in principle there is no reason to use floor. And in practice, due to precision of float number computation, this can sometime result in a smaller count of number of TRs. As long as the user provide the correct total_duration
Latest commit 9889b80 Sep 14, 2018

README.rst

Brain Imaging Analysis Kit

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The Brain Imaging Analysis Kit is a package of Python modules useful for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis.

The package was originally created by a collaboration between Intel and the Princeton Neuroscience Institute (PNI).

To reduce verbosity, we may refer to the Brain Imaging Analysis Kit using the BrainIAK abbreviation. Whenever lowercase spelling is used (e.g., Python package name), we use brainiak.

Quickstart

If you have Conda:

conda install -c brainiak -c defaults -c conda-forge brainiak

Otherwise, or if you want to compile from source, install the requirements (see docs/installation) and then install from PyPI:

python3 -m pip install brainiak

Note that we do not support Windows.

Docker

You can also test BrainIAK without installing it using Docker:

docker pull brainiak/brainiak
docker run -it -p 8888:8888 -v brainiak:/mnt --name demo brainiak/brainiak

To run Jupyter notebooks in the running container, try:

python3 -m notebook --allow-root --no-browser --ip=0.0.0.0

Then visit http://localhost:8888 in your browser and enter the token. Protip: run screen before running the notebook command.

Note that we do not support MPI execution using Docker containers and that performance will not be optimal.

Support

If you have a question or feedback, chat with us on Gitter or email our list at brainiak@googlegroups.com. If you find a problem with BrainIAK, you can also open an issue on GitHub.

Examples

We include BrainIAK usage examples in the examples directory of the code repository, e.g., funcalign/srm_image_prediction_example.ipynb.

To run the examples, download an archive of the latest BrainIAK release from GitHub. Note that we only support the latest release at this moment, so make sure to upgrade your BrainIAK installation.

Documentation

The documentation is available at http://brainiak.org/docs.

Contributing

We welcome contributions. Have a look at the issues labeled "easy" for starting contribution ideas. Please read the guide in CONTRIBUTING.rst first.

Citing

Please cite BrainIAK in your publications as: "Brain Imaging Analysis Kit, http://brainiak.org." Additionally, if you use RRIDs to identify resources, please mention BrainIAK as "Brain Imaging Analysis Kit, RRID:SCR_014824". Finally, please cite the publications referenced in the documentation of the BrainIAK modules you use, e.g., SRM.