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Changes to documentation in FAQs and built-in components
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synchon authored Sep 30, 2022
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221 changes: 182 additions & 39 deletions docs/builtin.rst
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.. include:: links.inc

Available pipeline steps
========================
Pipeline steps and atlases
==========================


Data Grabbers
^^^^^^^^^^^^^

..
..
Provide a list of the DataGrabbers that are implemented or planned.
Access: Valid options are
- Open
- Open with registration
- Restricted
Type/config: this should mention weather the class is built-in in the
core of junifer or needs to be imported from a specific configuration in
the `junifer.configs` module.
Expand All @@ -27,7 +28,10 @@ Data Grabbers
implementing the dataset. Links to github can be added by using the
following syntax: :gh:`<issue number>`

.. list-table:: Available data grabbers
Available
---------

.. list-table::
:widths: auto
:header-rows: 1

Expand All @@ -37,27 +41,72 @@ Data Grabbers
- Type/Config
- State
- Version Added
* - `DataladHCP1200`
* - :class:`junifer.datagrabber.DataladHCP1200`
- `HCP OpenAccess dataset <https://github.com/datalad-datasets/human-connectome-project-openaccess>`_
- Open with registration
- Built-in
- In Progress
- :gh:`4`
* - `JuselessDataladUKBVBM`
- UKB VBM dataset preprocessed with CAT. Available for Juseless only
* - :class:`junifer.configs.juseless.JuselessDataladUKBVBM`
- UKB VBM dataset preprocessed with CAT. Available for Juseless only.
- Restricted
- `junifer.configs.juseless`
- ``junifer.configs.juseless``
- Done
- 0.0.1
* - :class:`junifer.datagrabber.DataladAOMIC1000`
- `AOMIC 1000 dataset <https://github.com/OpenNeuroDatasets/ds003097>`_
- Open without registration
- Built-in
- Done
- 0.0.1
* - :class:`junifer.configs.juseless.JuselessDataladAOMICVBM`
- AOMIC VBM dataset. Available for Juseless only.
- Restricted
- ``junifer.configs.juseless``
- In Progress
- :gh:`57`


Planned
-------

.. list-table::
:widths: auto
:header-rows: 1

* - Name
- Description
- Access
- Type/Config
- Reference
* - CamCAN
- CamCAN dataset for Juseless
- Restricted
- ``junifer.configs.juseless``
- :gh:`46`
* - ENKI
- ENKI dataset for Juseless
- Restricted
- ``junifer.configs.juseless``
- :gh:`47`
* - IXI
- IXI dataset for Juseless
- Restricted
- ``junifer.configs.juseless``
- :gh:`48`
* - UCLA
- UCLA dataset for Juseless
- Built-in
- ``junifer.configs.juseless``
- :gh:`88`


Markers
^^^^^^^

..
..
Provide a list of the Markers that are implemented or planned.
State: this should indicate the state of the dataset. Valid options are
- Planned
- In Progress
Expand All @@ -68,7 +117,10 @@ Markers
implementing the dataset. Links to github can be added by using the
following syntax: :gh:`<issue number>`

.. list-table:: Available data grabbers
Available
---------

.. list-table::
:widths: auto
:header-rows: 1

Expand All @@ -80,33 +132,124 @@ Markers
- Apply parcellation and perform aggregation function
- Done
- 0.0.1
* - :class:`junifer.markers.FunctionalConnectivityAtlas`
- Compute functional connectivity
- Done
- 0.0.1
* - :class:`junifer.markers.SphereAggregation`
- Spherical aggregation using mean
- Done
- 0.0.1
* - :class:`junifer.markers.RSSETSMarker`
- Compute root sum of squares of edgewise timeseries
- Done
- 0.0.1


Planned
-------

.. list-table::
:widths: auto
:header-rows: 1

* - Name
- Description
- Reference
* - Connectedness
- Compute connectedness
- :gh:`34`
* - ALFF and (f)ALFF
- Detect amplitude of low-frequency fluctuation (ALFF) for resting-state fMRI
- :gh:`35`
* - ReHo
- Calculate regional homogeneity
- :gh:`36`
* - Permutation entropy, Range entropy, Multiscale entropy and Hurst exponent
- Calculate Permutation entropy, Range entropy, Multiscale entropy and Hurst exponent
- :gh:`61`
* - EdgeCentricFC
- Calculate edge-centric functional connectivity
- :gh:`64`
* - CrossAtlasFC
- Calculate cross-atlas functional connectivity
- :gh:`85`


Atlases
^^^^^^^

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` | |
+------------------+-----------------------+-----------------------------+---------------+
Available
---------

======== ================= ================================================================================= ============= ====================================================
Name Options Keys Version added Publication
======== ================= ================================================================================= ============= ====================================================
Schaefer ``n_rois``, | ``Schaefer900x7``, ``Schaefer1000x7``, ``Schaefer100x17``, ``Schaefer200x17``, 0.0.1 | Alexander Schaefer, Ru Kong, Evan M Gordon,
``yeo_networks`` | ``Schaefer300x17``, ``Schaefer400x17``, ``Schaefer500x17``, ``Schaefer600x17``, | Timothy O Laumann, Xi-Nian Zuo, Avram J Holmes,
| ``Schaefer700x17``, ``Schaefer800x17``, ``Schaefer900x17``, ``Schaefer1000x17`` | Simon B Eickhoff, B T Thomas Yeo. Local-Global
| Parcellation of the Human Cerebral Cortex from
| Intrinsic Functional Connectivity MRI, Cerebral
| Cortex, Volume 28, Issue 9, September 2018, Pages
| 3095–3114.
| https://doi.org/10.1093/cercor/bhx179
SUIT ``space`` | ``SUITxMNI``, ``SUITxSUIT`` 0.0.1 | Diedrichsen J. (2006). A spatially unbiased atlas
| template of the human cerebellum. NeuroImage,
| 33(1), 127–138.
| https://doi.org/10.1016/j.neuroimage.2006.05.056
TIAN ``scale``, | ``TianxS1x3TxMNI6thgeneration``, ``TianxS1x3TxMNInonlinear2009cAsym``, 0.0.1 | Tian, Y., Margulies, D.S., Breakspear, M. et al.
``space``, | ``TianxS1x7TxMNI6thgeneration``, ``TianxS2x3TxMNI6thgeneration``, | Topographic organization of the human subcortex
``magneticfield`` | ``TianxS2x3TxMNInonlinear2009cAsym``, ``TianxS2x7TxMNI6thgeneration``, | unveiled with functional connectivity gradients.
| ``TianxS3x3TxMNI6thgeneration``, ``TianxS3x3TxMNInonlinear2009cAsym``, | Nat Neurosci 23, 1421–1432 (2020).
| ``TianxS3x7TxMNI6thgeneration``, ``TianxS4x3TxMNI6thgeneration``, | https://doi.org/10.1038/s41593-020-00711-6
| ``TianxS4x3TxMNInonlinear2009cAsym``, ``TianxS4x7TxMNI6thgeneration``
======== ================= ================================================================================= ============= ====================================================


Planned
-------

================= ==============================================================================
Name 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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.. include:: links.inc

.. _contribution_guidelines:

Contributing to junifer
=======================

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FAQs
====

How do I contribute to junifer?
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Please follow the :ref:`contribution guidelines <contribution_guidelines>`.


How do I set up VSCode for contribution?
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

The :ref:`contribution guidelines <contribution_guidelines>`
apply in general when using VSCode as your IDE as well.

The following steps are specific to VSCode and you can choose to go with it:

1. After forking the repository on GitHub, you can clone the forked repository
using the internal version control tool.

2. We recommend using ``conda`` to create your virtual environment

.. code-block:: console
conda env create -n <your-environment-name> -f conda-env.yml python=3.9
conda activate <your-environment-name>
The ``conda-env.yml`` can be found at the root of the repository.

The required development tools should be installed and you should be good to go.

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