bids app using deepMReye to decode eye motion for fMRI time series data
Project description
bidsMReye
BIDS app for decoding gaze position from the eyeball MR-signal using deepMReye (1).
To be used on preprocessed BIDS derivatives (e.g. fMRIprep outputs). No eye-tracking data required.
By default, bidsMReye uses a pre-trained version of deepMReye trained on 5 datasets incl. guided fixations (2), smooth pursuit (3,4,5) and free viewing (6). Other pretrained versions are optional. Dedicated model training is recommended.
The pipeline automatically extracts the eyeball voxels and saves them as a python pickle file. This can be used also for other multivariate pattern analyses in the absence of eye-tracking data. Decoded gaze positions allow computing eye movements.
For more information, see the User Recommendations. If you have other questions, please reach out to the developer team.
Requirements
At the moment bidsmreye only supports python 3.8 and 3.9.
Install
Better to use the docker image as there are known install issues of deepmreye on Apple M1 for example.
Docker
Build
docker build --tag cpplab/bidsmreye:latest --file docker/Dockerfile .
Pull (work in progress)
Pull the latest docker image:
docker pull cpplab/bidsmreye:latest
Python package
You can also get the package from pypi if you want.
pip install bidsmreye
Conda installation
NOT TESTED YET
To encapsulate bidsMReye in a virtual environment install with the following commands:
conda create --name bidsmreye python=3.9
conda activate bidsmreye
pip install bidsmreye
The tensorflow dependency supports both CPU and GPU instructions.
Note that you might need to install cudnn first
conda install -c conda-forge cudnn
If installation of ANTsPy fails try to manually install it via:
git clone https://github.com/ANTsX/ANTsPy
cd ANTsPy
pip install CMake
python3 setup.py install
Dev install
Clone this repository.
git clone git://github.com/cpp-lln-lab/bidsmreye
Then install the package:
cd bidsMReye
make install_dev
Usage
CLI
Type the following for more information:
bidsmreye --help
--action prepapre
means that bidsmreye will extract the data coming from the
eyes from the fMRI images.
bidsmreye --action prepapre \
bids_dir \
output_dir
--action generalize
means that the extracted data will be used as input and
that bidsmeye will use it to predict what were the eye movements of your
participants.
bidsmreye --action generalize \
bids_dir \
output_dir
"all" does "prepare" then "generalize".
bidsmreye --action all \
bids_dir \
output_dir
Demo
Please look up the documentation
Contributors ✨
Thanks goes to these wonderful people (emoji key):
Pauline Cabee 💻 🤔 🚇 |
Remi Gau 💻 🤔 ⚠️ 🚧 |
This project follows the all-contributors specification. Contributions of any kind welcome!
If you train deepMReye, or if you have eye-tracking training labels and the extracted eyeball voxels, consider sharing it to contribute to the pretrained model pool.
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for bidsmreye-0.1.2-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 8e073910b52797602d6df729ed2b8173369dfd6be017b975606267c5b627d981 |
|
MD5 | bcf6c453610132f289b29e6cc744a8ad |
|
BLAKE2b-256 | 055a27a828e6f4b4b3454df94e84001440a9d86be8da26aa2dd30cdf791e9b14 |