Metadata-Version: 2.1
Name: bidsmreye
Version: 0.3.1
Summary: bids app using deepMReye to decode eye motion for fMRI time series data
Home-page: https://github.com/cpp-lln-lab/bidsMReye
Download-URL: https://github.com/cpp-lln-lab/bidsMReye
Author: Remi Gau
Maintainer: Remi Gau
Maintainer-email: remi.gau@gmail.com
License: LGPL-3.0
Keywords: BIDS,brain imaging data structure,neuroimaging,automated pipeline,MRI,Eyetracking,Machine learning
Platform: OS Independent # adapt given that untested on windows and problematic on Mac M1
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Topic :: Scientific/Engineering :: Image Processing
Provides: bidsmreye
Requires-Python: <3.11,>=3.8.0
Description-Content-Type: text/markdown
Provides-Extra: dev
Provides-Extra: doc
Provides-Extra: docs
Provides-Extra: style
Provides-Extra: styles
Provides-Extra: test
Provides-Extra: tests
License-File: LICENSE

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# bidsMReye

BIDS app for decoding gaze position from the eyeball MR-signal using
[deepMReye](https://github.com/DeepMReye/DeepMReye)
([1](https://doi.org/10.1038/s41593-021-00947-w)).

To be used on preprocessed BIDS derivatives (e.g.
[fMRIprep](https://github.com/nipreps/fmriprep) outputs).
No eye-tracking data required.

By default, bidsMReye uses a [pre-trained version](https://osf.io/mrhk9/) of
[deepMReye](https://github.com/DeepMReye/DeepMReye) trained on 5 datasets incl.
guided fixations ([2](https://doi.org/10.1038/sdata.2017.181)), smooth pursuit
([3](https://doi.org/10.1016/j.neuroimage.2018.04.012),[4](https://doi.org/10.1101/2021.08.03.454928),[5](https://doi.org/10.1038/s41593-017-0050-8))
and free viewing ([6](https://doi.org/10.1038/s41593-017-0049-1)). Other
pretrained versions are optional. Dedicated model training is recommended.

The pipeline automatically extracts the eyeball voxels.
This can be used also for other multivariate pattern
analyses in the absence of eye-tracking data.
Decoded gaze positions allow computing eye movements.

Some basic quality control and outliers detection is also performed:

- for each run

![](https://github.com/cpp-lln-lab/bidsMReye/blob/main/docs/source/images/sub-01_task-auditory_space-MNI152NLin6Asym_desc-bidsmreye_eyetrack.png)


- at the group level

![](https://github.com/cpp-lln-lab/bidsMReye/blob/main/docs/source/images/group_eyetrack.png)

For more information, see the
[User Recommendations](https://deepmreye.slite.com/p/channel/MUgmvViEbaATSrqt3susLZ/notes/kKdOXmLqe).
If you have other questions, please reach out to the developer team.

## Install

Better to use the docker image as there are known install issues
of deepmreye on Apple M1 for example.

### Docker

#### Build

```bash
docker build --tag cpplab/bidsmreye:latest --file docker/Dockerfile .
```

#### Pull

Pull the latest docker image:

```bash
docker pull cpplab/bidsmreye:latest
```

### Python package

You can also get the package from pypi if you want.

```bash
pip install bidsmreye
```

#### Conda installation

**NOT TESTED YET**

To encapsulate bidsMReye in a virtual environment install with the following commands:

```bash
conda create --name bidsmreye python=3.10
conda activate bidsmreye
conda install pip
pip install bidsmreye
```

The tensorflow dependency supports both CPU and GPU instructions.

Note that you might need to install cudnn first

```bash
conda install -c conda-forge cudnn
```

#### ANTsPy installation issues

If installation of [ANTsPy](https://github.com/ANTsX/ANTsPy) fails try to manually install it via:

<!-- may help on windows ? -->

```bash
git clone https://github.com/ANTsX/ANTsPy
cd ANTsPy
pip install CMake
python3 setup.py install
```

### Dev install

Clone this repository.

```bash
git clone git://github.com/cpp-lln-lab/bidsmreye
```

Then install the package:

```bash
cd bidsMReye
make install_dev
```

## Usage

## Requirements

bidsmreye requires your input fmri data:

 - to be minimally preprocessed (at least realigned),
 - with filenames and structure that conforms to a BIDS derivative dataset.

Two bids apps are available to generate those types of preprocessed data:

- [fmriprep](https://fmriprep.org/en/stable/)
- [bidspm](https://bidspm.readthedocs.io/en/latest/general_information.html)

Obviousvly your fmri data must include the eyes of your participant for bidsmreye to work.

<!-- old fmriprep versions may not work -->

### CLI

Type the following for more information:

```bash
bidsmreye --help
```

## Preparing the data

`--action prepapre` means that bidsmreye will extract the data coming from the
eyes from the fMRI images.

If your data is not in MNI space, bidsmreye will also register the data to MNI.

```bash
bidsmreye --action prepare \
          bids_dir \
          output_dir \
          participant
```

## Computing the eye movements

`--action generalize` use the extracted timeseries to predict the eye movements
using the default pre-trained model of deepmreye.

This will also generate a quality control report of the decoded eye movements.

```bash
bidsmreye --action generalize \
          bids_dir \
          output_dir \
          participant
```
## Doing it all at once

`--action all` does "prepare" then "generalize".

```bash
bidsmreye --action all \
          bids_dir \
          output_dir \
          participant
```

## Group level summary

bidsmreye --action qc \
          bids_dir \
          output_dir \
          group

## Demo

Please look up the [documentation](https://bidsmreye.readthedocs.io/en/latest/demo.html)

## Contributors ✨

Thanks goes to these wonderful people
([emoji key](https://allcontributors.org/docs/en/emoji-key)):

<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
<!-- prettier-ignore-start -->
<!-- markdownlint-disable -->
<table>
  <tr>
    <td align="center"><a href="https://weexee.github.io/Portfolio/"><img src="https://avatars.githubusercontent.com/u/91776803?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Pauline Cabee</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/bidsMReye/commits?author=WeeXee" title="Code">💻</a> <a href="#ideas-WeeXee" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-WeeXee" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
    <td align="center"><a href="https://remi-gau.github.io/"><img src="https://avatars.githubusercontent.com/u/6961185?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Remi Gau</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/bidsMReye/commits?author=Remi-Gau" title="Code">💻</a> <a href="#ideas-Remi-Gau" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/cpp-lln-lab/bidsMReye/commits?author=Remi-Gau" title="Tests">⚠️</a> <a href="#maintenance-Remi-Gau" title="Maintenance">🚧</a></td>
  </tr>
</table>

<!-- markdownlint-restore -->
<!-- prettier-ignore-end -->

<!-- ALL-CONTRIBUTORS-LIST:END -->

This project follows the
[all-contributors](https://github.com/all-contributors/all-contributors)
specification. Contributions of any kind welcome!

If you train [deepMReye](https://github.com/DeepMReye/DeepMReye), or if you have
eye-tracking training labels and the extracted eyeball voxels, consider sharing
it to contribute to the [pretrained model pool](https://osf.io/mrhk9/).
