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99 changes: 71 additions & 28 deletions docs/builtin.rst
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Available pipeline steps
========================
Available pipeline and atlases
==============================


Data Grabbers
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Available Atlases and Coordinates
=================================

+------------------+-----------------------+-----------------------------+---------------+
| Name | Options | Keys | Version Added |
+==================+=======================+=============================+===============+
| Schaefer | `n_rois` | `Schaefer100x7` | 0.0.1 |
| | `yeo_networks` | `Schaefer200x7` | |
| | | `Schaefer300x7` | |
| | | `Schaefer400x7` | |
| | | `Schaefer500x7` | |
| | | `Schaefer600x7` | |
| | | `Schaefer700x7` | |
| | | `Schaefer800x7` | |
| | | `Schaefer900x7` | |
| | | `Schaefer1000x7` | |
| | | `Schaefer100x17` | |
| | | `Schaefer200x17` | |
| | | `Schaefer300x17` | |
| | | `Schaefer400x17` | |
| | | `Schaefer500x17` | |
| | | `Schaefer600x17` | |
| | | `Schaefer700x17` | |
| | | `Schaefer800x17` | |
| | | `Schaefer900x17` | |
| | | `Schaefer1000x17` | |
+------------------+-----------------------+-----------------------------+---------------+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^



======== ============= ================================================================= =============
Name Options Keys Version added
======== ============= ================================================================= =============
Schaefer n_rois, | Schaefer900x7, Schaefer1000x7, Schaefer100x17, Schaefer200x17, 0.0.1
yeo_networks | Schaefer500x7, Schaefer600x7, Schaefer700x7, Schaefer800x7,
| Schaefer300x17, Schaefer400x17, Schaefer500x17, Schaefer600x17,
| Schaefer700x17, Schaefer800x17, Schaefer900x17, Schaefer1000x17
SUIT space SUITxMNI, SUITxSUIT 0.0.1
TIAN scale, | TianxS1x3TxMNI6thgeneration, TianxS1x3TxMNInonlinear2009cAsym,
space, | TianxS1x7TxMNI6thgeneration, TianxS2x3TxMNI6thgeneration,
magneticfield | TianxS2x3TxMNInonlinear2009cAsym, TianxS2x7TxMNI6thgeneration,
| TianxS3x3TxMNI6thgeneration, TianxS3x3TxMNInonlinear2009cAsym,
| TianxS3x7TxMNI6thgeneration, TianxS4x3TxMNI6thgeneration,
| TianxS4x3TxMNInonlinear2009cAsym, TianxS4x7TxMNI6thgeneration 0.0.1
======== ============= ================================================================= =============


Atlases under consideration
^^^^^^^^^^^^^^^^^^^^^^^^^^^


================= ==============================================================================
Atlas Names Publication
================= ==============================================================================
Desikan-Killiany | Desikan, R. S., Ségonne, F., Fischl, B., Quinn, B. T., Dickerson, B. C.,
| Blacker, D., et al. (2006). An automated labeling system for
| subdividing the human cerebral cortex on MRI scans into gyral based
| regions of interest. NeuroImage, 31(3), 968-980.
| http://doi.org/10.1016/j.neuroimage.2006.01.021
Glasser | Glasser, M. F., Coalson, T. S., Robinson, E. C., Hacker, C. D.,
| Harwell, J., Yacoub, E., et al. (2016). A multi-modal parcellation
| of human cerebral cortex. Nature.
| http://doi.org/10.1038/nature18933
AAL | Rolls, E. T., Huang, C. C., Lin, C. P., Feng, J., & Joliot, M. (2020).
| Automated anatomical labelling atlas 3. Neuroimage, 206, 116189.
| https://doi.org/10.1016/j.neuroimage.2019.116189
Shen | Shen X, Tokoglu F, Papademetris X, Constable RT. Groupwise whole-brain
| parcellation from resting-state fMRI data for network node identification.
| Neuroimage. 2013 Nov 15;82:403-15.
| https://doi.org/10.1016/j.neuroimage.2013.05.081.
Mindboggle 101 | Klein, A., & Tourville, J. (2012). 101 labeled brain images and a
| consistent human cortical labeling protocol. Frontiers in Neuroscience.
| http://doi.org/10.3389/fnins.2012.00171/abstract
Destrieux | Destrieux, C., Fischl, B., Dale, A., & Halgren, E. (2010). Automatic
| parcellation of human cortical gyri and sulci using standard anatomical
| nomenclature. NeuroImage, 53(1), 1–15.
| http://doi.org/10.1016/j.neuroimage.2010.06.010.
Fan | Fan, L., Li, H., Zhuo, J., Zhang, Y., Wang, J., Chen, L., ...
| & Jiang, T. (2016). The human brainnetome atlas: a new brain atlas based
| on connectional architecture. Cerebral cortex, 26(8), 3508-3526.
| https://doi.org/10.1093/cercor/bhw157
Buckner | Buckner, R. L., Krienen, F. M., Castellanos, A., Diaz, J. C.,
| & Yeo, B. T. T. (2011). The organization of the human cerebellum
| estimated by intrinsic functional connectivity. Journal of Neurophysiology,
| 106(5), 2322–2345.
| https://doi.org/10.1152/jn.00339.2011
| Yeo, B. T. T., Krienen, F. M., Sepulcre, J., Sabuncu, M. R., Lashkari, D.,
| Hollinshead, M., et al. (2011). The organization of the human cerebral
| cortex estimated by intrinsic functional connectivity.
| Journal of Neurophysiology, 106(3), 1125–1165.
| https://doi.org/10.1152/jn.00338.2011
================= ==============================================================================

..
helpful site for creating tables: https://rest-sphinx-memo.readthedocs.io/en/latest/ReST.html#tables
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FAQs
====

What are the first steps to contribute to junifer?
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* go to `contribution <https://juaml.github.io/junifer/main/contribution.html>`_ and follow the steps written here.


What is the easiest setup to contribute to junifer?
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Use VScode (or any other IDE (interactive developer environment) of your choice) with which you can fork the repository and git.

We followed the following steps to get started with contributing:

1. Fork the repository

* copy the link and do ``git-clone``

2. Create the development environment

* create the environment using conda ``conda env create -n {NameOfEnvironment} python=3.9``
* update the environment ``conda env update -n {NameOfEnvironment} --file=conda-env.yml``. The relevant file is within the junifer directory.
* activate the environment ``conda activate {NameOfEnvironment}``

3. install junifer

* go to your junifer-directory ``cd {junifer-directory}`` and ``pip install -e .``

4. open VS code and start contributing


P.S.: if you want to contribute to the documentation go to
`7.4 <file:///Users/pat/Desktop/junifer/junifer_BH/docs/_build/contribution.html#adding-and-building-documentation>`_ and build the packages required for documentation
``pip install -e ".[docs]"
cd docs
make local``
You can change the content of the html sites by changing the related .rst-files.
to check how your chagnes look like in your browser, save the .rst-file after changing and type ``make local``.
Afterwards, open the index.html file or other related html file in your browser



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