Reorganize docs

.gitignore

@@ -16,4 +16,7 @@ dist/
 .pytest_cache/
 _.py
 _.ipynb
-.idea
+.idea
+
+# sphinx documentation
+docs/_build/*

docs/diffusion.rst

@@ -30,7 +30,7 @@ Output Summary Table
     * - Tractography
       - tensor field
       - fiber tracts
-      - 
+      -
     * - Graph Generation
       - fiber tracts, parcellations
       - connectome
@@ -40,7 +40,7 @@ Output Summary Table
 Output subject-level pipeline summary
 =====================================
 
-.. figure:: ../_static/ndmg-d-detailed-pipeline.jpg
+.. figure:: ./_static/ndmg-d-detailed-pipeline.jpg
     :align: left
     :figwidth: 700px
 
@@ -58,7 +58,7 @@ The transform mapping the T1w volume to the template is then applied to the dMRI
 
 Finally, `NDMG` produces a QA plot showing three slices of the first BO volume of the aligned dMRI image overlaid on the MNI152 template in the three principle coordinate planes (Figure S2).
 
-.. figure:: ../_static/registration-qa.png
+.. figure:: ./_static/registration-qa.png
     :align: left
     :figwidth: 700px
 
@@ -74,7 +74,7 @@ Once the dMRI volumes have been aligned to the template, `NDMG` begins diffusion
 
 While high-dimensional diffusion models, such as orientation distribution functions (ODFs) or q-ball, enable reconstruction of crossing fibers and complex fiber trajectories, these methods are designed for images with a large number of diffusion volumes/directions for a given image. Because `NDMG` is designed to be robust across a wide range of dMRI studies, including diffusion tensor imaging, `NDMG` uses a lower-dimensional tensor model. The model, described in detail on DiPy_'s website, computes a 6-component tensor for each voxel in the image. This reduces the dMRI image stack to a single 6-dimensional image that can be used for tractography. `NDMG` generates a QA plot showing slices of the FA map derived from the tensors in nine panels, as below (Figure S3)
 
-.. figure:: ../_static/tensor-qa.png
+.. figure:: ./_static/tensor-qa.png
     :align: left
     :figwidth: 700px
 

docs/index.rst

@@ -9,7 +9,7 @@ Overview of m2g
 
 NeuroData’s MR Graphs package, `m2g`, is the successor of the MRCAP, MIGRAINE, and m2g pipelines. m2g combines dMRI, fMRI, and sMRI data from a single subject to estimate a high-level connectome reliably and scalably.
 
-The m2g pipeline has been developed as a one-click solution for human connectome estimation by providing robust and reliable estimates of connectivity across a wide range of datasets. The pipelines are explained and derivatives analyzed in our pre-print, available on BiorXiv_.
+The m2g pipeline has been developed as a one-click solution for human connectome estimation by providing robust and reliable estimates of connectivity across a wide range of datasets. The pipelines are explained and derivatives analyzed in our pre-print, available on BioRxiv_.
 
 Free software
 -------------

docs/license.rst

@@ -0,0 +1,137 @@
+License
+=======
+m2g is distributed with Polyform license.
+
+::
+
+    # PolyForm Noncommercial License 1.0.0
+
+    <https://polyformproject.org/licenses/noncommercial/1.0.0>
+
+    ## Acceptance
+
+    In order to get any license under these terms, you must agree
+    to them as both strict obligations and conditions to all
+    your licenses.
+
+    ## Copyright License
+
+    The licensor grants you a copyright license for the
+    software to do everything you might do with the software
+    that would otherwise infringe the licensor's copyright
+    in it for any permitted purpose.  However, you may
+    only distribute the software according to [Distribution
+    License](#distribution-license) and make changes or new works
+    based on the software according to [Changes and New Works
+    License](#changes-and-new-works-license).
+
+    ## Distribution License
+
+    The licensor grants you an additional copyright license
+    to distribute copies of the software.  Your license
+    to distribute covers distributing the software with
+    changes and new works permitted by [Changes and New Works
+    License](#changes-and-new-works-license).
+
+    ## Notices
+
+    You must ensure that anyone who gets a copy of any part of
+    the software from you also gets a copy of these terms or the
+    URL for them above, as well as copies of any plain-text lines
+    beginning with `Required Notice:` that the licensor provided
+    with the software.  For example:
+
+    > Required Notice: Copyright Yoyodyne, Inc. (http://example.com)
+
+    ## Changes and New Works License
+
+    The licensor grants you an additional copyright license to
+    make changes and new works based on the software for any
+    permitted purpose.
+
+    ## Patent License
+
+    The licensor grants you a patent license for the software that
+    covers patent claims the licensor can license, or becomes able
+    to license, that you would infringe by using the software.
+
+    ## Noncommercial Purposes
+
+    Any noncommercial purpose is a permitted purpose.
+
+    ## Personal Uses
+
+    Personal use for research, experiment, and testing for
+    the benefit of public knowledge, personal study, private
+    entertainment, hobby projects, amateur pursuits, or religious
+    observance, without any anticipated commercial application,
+    is use for a permitted purpose.
+
+    ## Noncommercial Organizations
+
+    Use by any charitable organization, educational institution,
+    public research organization, public safety or health
+    organization, environmental protection organization,
+    or government institution is use for a permitted purpose
+    regardless of the source of funding or obligations resulting
+    from the funding.
+
+    ## Fair Use
+
+    You may have "fair use" rights for the software under the
+    law. These terms do not limit them.
+
+    ## No Other Rights
+
+    These terms do not allow you to sublicense or transfer any of
+    your licenses to anyone else, or prevent the licensor from
+    granting licenses to anyone else.  These terms do not imply
+    any other licenses.
+
+    ## Patent Defense
+
+    If you make any written claim that the software infringes or
+    contributes to infringement of any patent, your patent license
+    for the software granted under these terms ends immediately. If
+    your company makes such a claim, your patent license ends
+    immediately for work on behalf of your company.
+
+    ## Violations
+
+    The first time you are notified in writing that you have
+    violated any of these terms, or done anything with the software
+    not covered by your licenses, your licenses can nonetheless
+    continue if you come into full compliance with these terms,
+    and take practical steps to correct past violations, within
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+    end immediately.
+
+    ## No Liability
+
+    ***As far as the law allows, the software comes as is, without
+    any warranty or condition, and the licensor will not be liable
+    to you for any damages arising out of these terms or the use
+    or nature of the software, under any kind of legal claim.***
+
+    ## Definitions
+
+    The **licensor** is the individual or entity offering these
+    terms, and the **software** is the software the licensor makes
+    available under these terms.
+
+    **You** refers to the individual or entity agreeing to these
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+
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+    organizations that have control over, are under the control of,
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+    means ownership of substantially all the assets of an entity,
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+
+    **Your licenses** are all the licenses granted to you for the
+    software under these terms.
+
+    **Use** means anything you do with the software requiring one
+    of your licenses.