Update read the docs (#35)

* add readthedocs.yaml to kick of setup
* added movies
* update docstrings, remove unused methods
* added animations of defaced images
* bump version and tag

docs/index.rst

@@ -6,6 +6,24 @@
 Welcome to petdeface's documentation!
 =====================================
 
+petdeface is a nipype implementation of an anatomical MR and PET defacing pipeline for BIDS datasets. 
+This is a working prototype, in active development denoted by the 0.x.x version number. 
+
+.. image:: _static/3d_rotate.gif
+   :align: center
+
+|
+
+Petdface can be used to deface PET and MR data as well as co-register the two modalities. 
+Use is encouraged and feedback via Github issues or email to openneuropet@gmail.com is more than welcome. 
+As is often the case, this medical research software is constrained to testing on data that its developers 
+have access to.
+
+This software can be installed via source or via pip from PyPi with ``pip install petdeface``
+
+**NOTE:** This project is currently in beta release, some features listed below may 
+not be available for version numbers < 1.0.0
+
 .. toctree::
    installation
    modules
@@ -20,3 +38,28 @@ Indices and tables
 * :ref:`genindex`
 * :ref:`modindex`
 * :ref:`search`
+
+Citations
+---------
+
+1. Dale A, Fischl B, Sereno MI. Cortical Surface-Based Analysis: I. Segmentation and Surface Reconstruction.
+   Neuroimage. 1999;9(2):179–94. doi:10.1006/nimg.1998.0395.
+2. Fischl B. FreeSurfer. Neuroimage. 2012 Aug 15;62(2):774-81. doi: 10.1016/j.neuroimage.2012.01.021.
+   Epub 2012 Jan 10. PMID: 22248573; PMCID: PMC3685476.
+3. Stefano Cerri, Douglas N. Greve, Andrew Hoopes, Henrik Lundell, Hartwig R. Siebner, Mark Mühlau, Koen Van Leemput,
+   An open-source tool for longitudinal whole-brain and white matter lesion segmentation,
+   NeuroImage: Clinical, Volume 38, 2023, 103354, ISSN 2213-1582, https://doi.org/10.1016/j.nicl.2023.103354.
+   (https://www.sciencedirect.com/science/article/pii/S2213158223000438)
+4. Gorgolewski, Krzysztof J. ; Esteban, Oscar ; Burns, Christopher ; Ziegler, Erik ; Pinsard, Basile ; Madison, Cindee ;
+   Waskom, Michael ; Ellis, David Gage ; Clark, Dav ; Dayan, Michael ; Manhães-Savio, Alexandre ;
+   Notter, Michael Philipp ; Johnson, Hans ; Dewey, Blake E ; Halchenko, Yaroslav O. ; Hamalainen, Carlo ;
+   Keshavan, Anisha ; Clark, Daniel ; Huntenburg, Julia M. ; Hanke, Michael ; Nichols, B. Nolan ; Wassermann , Demian ;
+   Eshaghi, Arman ; Markiewicz, Christopher ; Varoquaux, Gael ; Acland, Benjamin ; Forbes, Jessica ; Rokem, Ariel ;
+   Kong, Xiang-Zhen ; Gramfort, Alexandre ; Kleesiek, Jens ; Schaefer, Alexander ; Sikka, Sharad ;
+   Perez-Guevara, Martin Felipe ; Glatard, Tristan ; Iqbal, Shariq ; Liu, Siqi ; Welch, David ; Sharp, Paul ;
+   Warner, Joshua ; Kastman, Erik ; Lampe, Leonie ; Perkins, L. Nathan ; Craddock, R. Cameron ; Küttner, René ;
+   Bielievtsov, Dmytro ; Geisler, Daniel ; Gerhard, Stephan ; Liem, Franziskus ; Linkersdörfer, Janosch ;
+   Margulies, Daniel S. ; Andberg, Sami Kristian ; Stadler, Jörg ; Steele, Christopher John ; Broderick, William ;
+   Cooper, Gavin ; Floren, Andrew ; Huang, Lijie ; Gonzalez, Ivan ; McNamee, Daniel ; Papadopoulos Orfanos, Dimitri ;
+   Pellman, John ; Triplett, William ; Ghosh, Satrajit (2016). Nipype: a flexible, lightweight and extensible
+   neuroimaging data processing framework in Python. 0.12.0-rc1. Zenodo. 10.5281/zenodo.50186

docs/installation.rst

@@ -17,6 +17,12 @@ Or cloned and installed from source::
     pip install dist/petdeface-<X.X.X>-py3-none-any.whl 
     # where X.X.X is the version number of the generated file
 
+.. raw:: html
+
+    <script async id="asciicast-626689" src="https://asciinema.org/a/626689.js"
+    async data-autoplay="true" data-speed="1.5" data-loop="true"></script>
+
+
 Dependencies
 ------------
 

docs/usage.rst

@@ -10,6 +10,11 @@ After installation PETdeface can be run from as follows::
 
     petdeface /inputfolder --output_dir /outputfolder
 
+.. raw:: html
+
+    <script async id="asciicast-626691" src="https://asciinema.org/a/626691.js"
+    async data-autoplay="true" data-speed="1.5" data-loop="true"></script>
+
 Given a PET BIDS dataset like below::
 
     tree /inputfolder
@@ -69,8 +74,8 @@ Previously faced files are replaced with defaced images while the registration,
 
 When viewed, a succesfully defaced PET image will have varying intensities in the face region, as shown below:
 
-.. image:: /_static/defaced_pet_side_view.png
-   :align: left
+.. image:: /_static/sagittal.gif
+    :align: left
 
 -----------------
 
@@ -123,14 +128,21 @@ Alternatively, if one is unable to install PETdeface from source or PIP, but can
     -v /Data/defaced_pet_data/:/output \
     -v /home/user/freesurfer/license.txt:/opt/freesurfer/license.txt \
     --platform linux/amd64 \
-    petdeface:latest  /input --output_dir /output --n_procs 16 --skip_bids_validator  --placement adjacent --user=$UID:$GID system_platform=Linux
+    petdeface:latest  /input \
+    --output_dir /output \
+    --n_procs 16 \
+    --skip_bids_validator \
+    --placement adjacent \
+    --user=$UID:$GID \
+    system_platform=Linux
 
 One needs to create 3 bind mounts to the docker container when running PETdeface directly from docker:
+
 1. /input needs to mounted to the input BIDS dataset on the host machine
 2. /output needs to be mounted to the output directory on the host machine
 3. /opt/freesurfer/license.txt needs to be mounted to the freesurfer license file on the host machine
 
 If one is running PETdeface on a linux machine and desires non-root execution of the container, 
-the `--user` flag needs to be set to the UID and GID of the user running the container.
+the ``--user`` flag needs to be set to the UID and GID of the user running the container.
 
-Of course all of the above is done automatically when running PETdeface using the `--docker` flag.
+Of course all of the above is done automatically when running PETdeface using the ``--docker`` flag.