diff --git a/.readthedocs.yaml b/.readthedocs.yaml index f4e5e39..45b17a7 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -14,7 +14,7 @@ build: # https://python-poetry.org/docs/managing-dependencies/#dependency-groups # VIRTUAL_ENV needs to be set manually for now. # See https://github.com/readthedocs/readthedocs.org/pull/11152/ - - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs + - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs --all-extras sphinx: configuration: docs/source/conf.py \ No newline at end of file diff --git a/README.md b/README.md index a2ea133..79d50c6 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,13 @@ -[![PyPI version preprocessing](https://badge.fury.io/py/brainles-preprocessing.svg)](https://pypi.python.org/pypi/brainles-preprocessing/) -[![Documentation Status](https://readthedocs.org/projects/brainles-preprocessing/badge/?version=latest)](http://brainles-preprocessing.readthedocs.io/?badge=latest) -[![tests](https://github.com/BrainLesion/preprocessing/actions/workflows/tests.yml/badge.svg)](https://github.com/BrainLesion/preprocessing/actions/workflows/tests.yml) # BrainLes-Preprocessing +[![Python Versions](https://img.shields.io/pypi/pyversions/brainles-preprocessing)](https://pypi.org/project/brainles-preprocessing/) +[![Stable Version](https://img.shields.io/pypi/v/brainles-preprocessing?label=stable)](https://pypi.python.org/pypi/brainles-preprocessing/) +[![Documentation Status](https://readthedocs.org/projects/brainles-preprocessing/badge/?version=latest)](http://brainles-preprocessing.readthedocs.io/?badge=latest) +[![tests](https://github.com/BrainLesion/preprocessing/actions/workflows/tests.yml/badge.svg)](https://github.com/BrainLesion/preprocessing/actions/workflows/tests.yml) + + + `BrainLes preprocessing` is a comprehensive tool for preprocessing tasks in biomedical imaging, with a focus on (but not limited to) multi-modal brain MRI. It can be used to build to build modular preprocessing pipelines: This includes **normalization**, **co-registration**, **atlas registration** and **skulstripping / brain extraction**. @@ -25,11 +29,20 @@ pip install brainles-preprocessing ## Usage -Please have a look at our [Jupyter Notebook tutorials](https://github.com/BrainLesion/tutorials/tree/main/preprocessing) illustrating the usage of BrainLes preprocessing. +A minimal example can be found following these badges: +[![nbviewer](https://raw.githubusercontent.com/jupyter/design/master/logos/Badges/nbviewer_badge.svg)](https://nbviewer.org/github/BrainLesion/tutorials/blob/main/preprocessing/preprocessing_tutorial.ipynb) + + Open In Colab + + + +For further information please have a look at our [Jupyter Notebook tutorials](https://github.com/BrainLesion/tutorials/tree/main/preprocessing) illustrating the usage of BrainLes preprocessing. +## Documentation +We provide a (WIP) documentation. Have a look [here](https://brainles-preprocessing.readthedocs.io/en/latest/?badge=latest) ## FAQ Please credit the authors by citing their work. diff --git a/docs/source/registration.rst b/docs/source/registration.rst index 536cadf..fe3405a 100644 --- a/docs/source/registration.rst +++ b/docs/source/registration.rst @@ -8,7 +8,19 @@ registration.registrator .. automodule:: brainles_preprocessing.registration.registrator +registration.ANTs +-------------------------------------- + +.. automodule:: brainles_preprocessing.registration.ANTs.ANTs + + +registration.eReg +-------------------------------------- + +.. automodule:: brainles_preprocessing.registration.eReg.eReg + + registration.niftyreg -------------------------------------- -.. automodule:: brainles_preprocessing.registration.niftyreg +.. automodule:: brainles_preprocessing.registration.niftyreg.niftyreg