Fill in README.

README.rst

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+#################
+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.

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