update docs

Author: josephmje

docs/index.rst

@@ -1,18 +1,20 @@
-Welcome to dmriprep's documentation!
-====================================
+..include:: links.rst
+..include:: ../README.rst
+../include:: license.rst
+
+Contents
+--------
 
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
 
-   readme
    installation
    changes
    usage
    workflows
    outputs
    contributing
-   authors
 
 Indices and tables
 ==================

docs/license.rst

@@ -0,0 +1,11 @@
+License information
+-------------------
+
+We use the 3-clause BSD license; the full license may be found in the
+`LICENSE <https://github.com/josephmje/dmriprep/blob/master/LICENSE>`_ file
+in the ``dmriprep`` distribution.
+
+All trademarks referenced herein are property of their respective holders.
+
+Copyright (c) 2018-2019, the dMRIPrep.
+All rights reserved.

docs/readme.rst

@@ -1,3 +1,5 @@
+.. include:: links.rst
+
 Usage
 -----
 
@@ -9,12 +11,31 @@ that is to be processed.
 The input dataset is required to be in valid :abbr:`BIDS (Brain Imaging Data
 Structure)` format, and it must include at least one T1w structural image and
 a dwi series.
+
+.. code-block:: console
+
+    bids
+    └── sub-01
+      ├── anat
+      │   └── sub-01_T1w.nii.gz
+      ├── dwi
+      │   ├── sub-01_dwi.bval
+      │   ├── sub-01_dwi.bvec
+      │   ├── sub-01_dwi.json
+      │   └── sub-01_dwi.nii.gz
+      └── fmap
+          ├── sub-01_acq-dwi_dir-AP_epi.json
+          ├── sub-01_acq-dwi_dir-AP_epi.nii.gz
+          ├── sub-01_acq-dwi_dir-PA_epi.json
+          └── sub-01_acq-dwi_dir-PA_epi.nii.gz
+
 We highly recommend that you validate your dataset with the free, online
 `BIDS Validator <http://bids-standard.github.io/bids-validator/>`_.
 
 The exact command to run ``dmriprep`` depends on the Installation_ method.
 The common parts of the command follow the `BIDS-Apps
 <https://github.com/BIDS-Apps>`_ definition.
+
 Example: ::
 
     dmriprep data/bids_root/ out/ participant -w work/

docs/usage.rst

@@ -1,2 +1,2 @@
-Workflows
-=========
+Processing pipeline details
+===========================