diff --git a/README.md b/README.md deleted file mode 100644 index 721069e..0000000 --- a/README.md +++ /dev/null @@ -1,2 +0,0 @@ -# fmripost-template -A generic fMRIPost workflow diff --git a/README.rst b/README.rst new file mode 100644 index 0000000..e0313cf --- /dev/null +++ b/README.rst @@ -0,0 +1,42 @@ +################# +fMRIPost-template +################# + +A generic fMRIPost workflow. + +******** +Overview +******** + +fMRIPost-template is a template repository that can be used to create new fMRIPost workflows. + +The workflows and functions in this repository are designed to implement the majority of +general-purpose steps in an fMRIPost pipeline. +Here are a few of the key features: + +1. Configuration files to define expected BIDS derivatives from the preprocessing pipeline. +2. Functions to collect and organize data from the BIDS derivatives. +3. The ability to work with the following preprocessing configurations: + + - fMRIPrep with ``--level full`` and the required output space for the fMRIPost workflow. + For example, fMRIPost-AROMA requires outputs in ``MNI152NLin6Asym`` space with + 2x2x2 mm voxels. + - fMRIPrep with ``--level full`` and boldref-space outputs, + along with transforms to the required output space for the fMRIPost workflow. + - fMRIPrep with ``--level full`` and boldref-space outputs, + along with transforms to spaces that can be combined with existing transforms to + required spaces. + For example, users may apply fMRIPost-AROMA to boldref derivatives with transforms to + MNI152NLin2009cAsym space. + In this case, the fMRIPost-AROMA workflow will pull a transform from MNI152NLin2009cAsym + to MNI152NLin6Asym from TemplateFlow and apply it, + along with the boldref-to-MNI152NLin2009cAsym transform, to the boldref-space derivatives. + + .. warning:: + + Currently, minimal- and resampling-level fMRIPrep derivatives are not supported, + as fMRIPost workflows typically require confounds that are only generated with + ``--level full``. + +4. General NiPreps infrastructure for running a BIDS App, such as a config file, + a command-line interface, and tools to generate HTML reports. diff --git a/docs/conf.py b/docs/conf.py index 9ccdc84..465bec9 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -10,6 +10,16 @@ # All configuration values have a default; values that are commented out # serve to show the default. +# Notes on fMRIPost-template-specific style: +# 1. For rst headings, we use the following convention, based on +# https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html#sections: +# # with overline, for parts +# * with overline, for chapters +# = for sections +# - for subsections +# ^ for subsubsections +# " for paragraphs + import os import sys