diff --git a/README.md b/README.md index 190ee60d4..848b7fd57 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,4 @@ -tedana: TE Dependent ANAlysis -============================= +# tedana: TE Dependent ANAlysis The ``tedana`` package is part of the ME-ICA pipeline, performing TE-dependent analysis of multi-echo functional magnetic resonance imaging (fMRI) data. @@ -15,41 +14,57 @@ multi-echo functional magnetic resonance imaging (fMRI) data. [![Codecov](https://codecov.io/gh/me-ica/tedana/branch/master/graph/badge.svg)](https://codecov.io/gh/me-ica/tedana) [![Join the chat at https://gitter.im/ME-ICA/tedana](https://badges.gitter.im/ME-ICA/tedana.svg)](https://gitter.im/ME-ICA/tedana?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) -About ------ +## About ``tedana`` originally came about as a part of the [ME-ICA](https://github.com/me-ica/me-ica) pipeline. The ME-ICA pipeline originally performed both pre-processing and TE-dependent analysis of multi-echo fMRI data; however, ``tedana`` now assumes that you're working with data which has been previously preprocessed. -If you're in need of a preprocessing pipeline, we recommend -[fmriprep](https://github.com/poldracklab/fmriprep/), which has been tested -for compatibility with multi-echo fMRI data and ``tedana``. ![http://tedana.readthedocs.io/](https://user-images.githubusercontent.com/7406227/40031156-57b7cbb8-57bc-11e8-8c51-5b29f2e86a48.png) -Installation ------------- +More information and documentation can be found at https://tedana.readthedocs.io/. -You'll need to set up a working development environment to use ``tedana``. -To set up a local environment, you will need Python >=3.6 and the following -packages will need to be installed: +## Installation -- mdp -- nilearn -- nibabel>=2.1.0 -- numpy -- scikit-learn -- scipy +You'll need to set up a working development environment to use `tedana`. +To set up a local environment, you will need Python >=3.6 and the following packages will need to be installed: -You can then install ``tedana`` with: +[mdp](https://pypi.org/project/MDP/) +[numpy](http://www.numpy.org/) +[scikit-learn](http://scikit-learn.org/stable/) +[scipy](https://www.scipy.org/) +[nilearn](https://nilearn.github.io/) +[nibabel>=2.1.0](http://nipy.org/nibabel/) + +You can then install `tedana` with + +```bash +pip install tedana +``` + +### Creating a miniconda environment for use with `tedana` +In using `tedana`, you can optionally configure [a conda environment](https://conda.io/docs/user-guide/tasks/manage-environments.html). + +We recommend using [miniconda3](https://conda.io/miniconda.html). +After installation, you can use the following commands to create an environment for `tedana`: ```bash +conda create -n ENVIRONMENT_NAME python=3 pip mdp numpy scikit-learn scipy nilearn nibabel +source activate ENVIRONMENT_NAME pip install tedana ``` -Getting involved ----------------- +`tedana` will then be available in your path. +This will also allow any previously existing tedana installations to remain untouched. + +To exit this conda environment, use + +```bash +source deactivate +``` + +## Getting involved We :yellow_heart: new contributors! To get started, check out [our contributing guidelines](https://github.com/ME-ICA/tedana/blob/master/CONTRIBUTING.md). diff --git a/docs/contributing.rst b/docs/contributing.rst index 34cdad2a9..38d9f19bb 100644 --- a/docs/contributing.rst +++ b/docs/contributing.rst @@ -11,9 +11,14 @@ For a more practical guide to the tedana development, please see our Governance ---------- +<<<<<<< HEAD Governance is a hugely important part of any project. It is especially important to have clear process and communication channels for open source projects that rely on a distributed network of volunteers, such as ``tedana``. +======= +Style Guide +=========== +>>>>>>> upstream/master ```tedana`` is currently supported by a small group of five core developers. Even with only five members involved in decision making processes, @@ -165,7 +170,11 @@ More information about what is required for a release to proceed is available in .. _release checklist: Release Checklist +<<<<<<< HEAD """"""""""""""""" +======= +================= +>>>>>>> upstream/master This is the checklist of items that must be completed when cutting a new release of tedana. These steps can only be completed by a project maintainer, but they are a good resource for diff --git a/docs/index.rst b/docs/index.rst index d3eac653d..d313472dc 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -129,11 +129,12 @@ tedana is licensed under GNU Lesser General Public License version 2.1. :maxdepth: 2 :caption: Contents: + installation multi-echo usage - installation approach outputs + support contributing roadmap api diff --git a/docs/installation.rst b/docs/installation.rst index 82fc724a0..7645b9859 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -17,19 +17,3 @@ You can then install ``tedana`` with: .. code-block:: bash pip install tedana - -Getting involved ----------------- - -We 💛 new contributors! -To get started, check out `our contributing guidelines`_. - -Want to learn more about our plans for developing ``tedana``? -Have a question, comment, or suggestion? -Open or comment on one of `our issues`_! - -We ask that all contributions to ``tedana`` respect our `code of conduct`_. - -.. _our contributing guidelines: https://github.com/ME-ICA/tedana/blob/master/CONTRIBUTING.md -.. _our issues: https://github.com/ME-ICA/tedana/issues -.. _code of conduct: https://github.com/ME-ICA/tedana/blob/master/CODE_OF_CONDUCT.md diff --git a/docs/support.rst b/docs/support.rst new file mode 100644 index 000000000..0828ea5c8 --- /dev/null +++ b/docs/support.rst @@ -0,0 +1,10 @@ +Support and Communication +------------------------- +All bugs, concerns and enhancement requests for this software can be submitted here: https://github.com/ME-ICA/tedana/issues. + +If you would like to ask a question about usage or tedana's outputs, please submit a question to `NeuroStars`_ with the ``multi-echo`` tag. + +All previous tedana-related questions are available `here`_. + +.. _NeuroStars: https://neurostars.org +.. _here: https://neurostars.org/tags/multi-echo