interim code and docs restructure

Author: jsheunis

assets/example_WM_mask.png

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 1d24c5085b479786d0d6d8522d56caea
+config: 87b99ee67b659e8076669993d66ca589
 tags: 645f666f9bcd5a90fca523b33c5a78b7

assets/example_brain_mask.png

@@ -6,6 +6,8 @@
 fMRwhy: BIDS-compatible fMRI analysis with SPM12
 ================================================
 
+``fMRwhy`` is a MATLAB- and SPM12-based toolbox with a variety of helper functions and BIDS-compatible workflows to assist in your fMRI quality checking, preprocessing and analysis journey.
+
 .. image:: http://img.shields.io/badge/license-LGPL--2.1-blue.svg
    :target: https://opensource.org/licenses/LGPL-2.1
    :alt: License
@@ -21,56 +23,30 @@ About
 .. image:: ../assets/fmrwhy_logo_2020.png
   :target: https://fmrwhy.readthedocs.io/
 
-``fMRwhy`` is a Matlab- and SPM12-based toolbox with a variety of helper functions and BIDS-compatible workflows to assist in your fMRI quality checking, preprocessing and analysis journey.
 
 With ``fMRwhy`` you are provided with the tools and shown *how* to calculate interesting quality metrics, *how* to visualize outcomes, *how* to analyse your data with batch scripts, and *how* to build a BIDS compatible analysis pipeline, all to flexible levels of automation.
 ``fMRwhy`` does not help with the *why* questions, which are arguably the most important ones that need to be considered right at the start of your fMRI research journey.
 
-``fMRwhy`` currently has the following features:
-
-Focus on functional MRI
-```````````````````````
-
-``fMRwhy`` was created with a core focus on functional MRI and basic structural (i.e. T1-weighted) preprocessing applications.
-
-BIDS-compatibility
-``````````````````
-
-``fMRwhy`` strives to stay compatible with the `Brain Imaging Data Structure`_.
-This includes understanding the structure of a BIDS dataset, such as the number and names of subjects, sessions, tasks, runs, and more.
-This compatibility allows automated pipelines to be run for any fMRI-based BIDS dataset.
-Additionally, ``fMRwhy`` will output derivative data in a BIDS-compatible fashion.
-
-Visual fMRI quality control
-````````````````````````````
-
-This is currently the core functionality. ``fmrwhy_bids_workflowQC`` is an automated, BIDS-compatible quality checking and reporting pipeline that generates subject-specific fMRI quality reports. An example is available `here`_.
-It requires a settings file to be prepopulated by the user based on the data and the user's preferences for processing steps. It can run on a full BIDS dataset with T1w and BOLD data, and will automatically derive the structure of the data in order to process all tasks, sessions and runs.
-Detailed usage information is available here, and the function's API is available here.
-
-Multi-echo fMRI preprocessing
-`````````````````````````````
-
-Multi-echo fMRI has known benefits for improving fMRI signal recovery, increasing the signal-to-noise ratio, and separating BOLD and non-BOLD fluctuations.
-``fMRwhy`` aims to make multi-echo processing methods accessible to researchers using SPM12 and Matlab.
-For this, much inspiration is drawn from the `tedana community`_.
-
-Accessible and extensible SPM12 batch processing
-````````````````````````````````````````````````
+``fMRwhy`` currently has the following `features`_:
 
-In an attempt to help users move from clicking through a GUI to building reproducible SPM12 analysis scripts,
-``fMRwhy`` makes SPM12 batch processes and other functions available as extensible functions. This includes standard SPM12 functionality such as realignment, reslicing, smoothing, and more.
+* Focus on functional MRI
+* BIDS-compatibility
+* Visual fMRI quality control
+* Multi-echo fMRI preprocessing
+* Accessible and extensible SPM12 batch processing
+* Processing utilities
 
-Processing utilities
-`````````````````````
+.. _features: https://fmrwhy.readthedocs.io/features.html
 
-Many helper functions are also available to assist with preprocessing, image calculation and visualization scripts. To find out more, please see the `API`_.
+Background
+----------
 
+``fMRwhy`` started as a loose collection of MATLAB- and SPM12-based scripts created to reproduce useful quality control measures and interesting visualizations as reported in journal articles,
+such as calculating the temporal signal-to-noise ratio of an fMRI time series or creating a carpet plot from fMRI data.
+The core idea behind this was: if the results of our research are supported by useful quality control methods, why not implement these in a reproducible and extensible way so that the greater community can benefit from and contribute to it?
+This evolved over time into a modular set of SPM12 batch process wrapper functions that simplified the process of creating reproducible fMRI preprocessing and quality reporting scripts.
+With the goal of allowing automated quality reporting workflows, BIDS-compatibility was added using ``bids-matlab`` as a dependency.
 
-.. _Brain Imaging Data Structure: https://bids.neuroimaging.io/
-.. _here: https://jsheunis.github.io/fmrwhy_sample_QCreport.html
-.. _tedana community: https://tedana.readthedocs.io/
-.. _API: https://fmrwhy.readthedocs.io/en/latest/#api
 
 License Information
 -------------------
@@ -82,10 +58,10 @@ License Information
    :maxdepth: 2
    :caption: Contents:
 
+   features
    installation
    quality
    multiecho
-   preprocessing
    resources
    contributing
    api

assets/example_carpet_plot.png

@@ -82,10 +82,10 @@
 
               <p class="caption"><span class="caption-text">Contents:</span></p>
 <ul>
+<li class="toctree-l1"><a class="reference internal" href="features.html">Core Features</a></li>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="quality.html">Quality Reporting</a></li>
 <li class="toctree-l1"><a class="reference internal" href="multiecho.html">Multi-echo processing</a></li>
-<li class="toctree-l1"><a class="reference internal" href="preprocessing.html">Preprocessing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="resources.html">Resources</a></li>
 <li class="toctree-l1"><a class="reference internal" href="contributing.html">Contributing to <code class="docutils literal notranslate"><span class="pre">fMRwhy</span></code></a></li>
 <li class="toctree-l1"><a class="reference internal" href="api.html">API</a></li>
@@ -156,22 +156,49 @@
 <h1 id="index">Index</h1>
 
 <div class="genindex-jumpbox">
- <a href="#C"><strong>C</strong></a>
- | <a href="#F"><strong>F</strong></a>
+ <a href="#F"><strong>F</strong></a>
 
 </div>
-<h2 id="C">C</h2>
+<h2 id="F">F</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api.html#module-code">code (module)</a>
+      <li><a href="api.html#module-fmrwhy.batch">fmrwhy.batch (module)</a>
+</li>
+      <li><a href="api.html#module-fmrwhy.bidsutils">fmrwhy.bidsutils (module)</a>
+</li>
+      <li><a href="api.html#module-fmrwhy.multiecho">fmrwhy.multiecho (module)</a>
+</li>
+      <li><a href="api.html#module-fmrwhy.qc">fmrwhy.qc (module)</a>
+</li>
+      <li><a href="api.html#module-fmrwhy.realtime">fmrwhy.realtime (module)</a>
+</li>
+      <li><a href="api.html#module-fmrwhy.settings">fmrwhy.settings (module)</a>
+</li>
+      <li><a href="api.html#module-fmrwhy.utils">fmrwhy.utils (module)</a>
+</li>
+      <li><a href="api.html#module-fmrwhy.workflows">fmrwhy.workflows (module)</a>
+</li>
+      <li><a href="api.html#fmrwhy.bidsutils.fmrwhy_bids_constructFilename">fmrwhy_bids_constructFilename() (in module fmrwhy.bidsutils)</a>
 </li>
   </ul></td>
-</tr></table>
-
-<h2 id="F">F</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api.html#code.fmrwhy_bids_constructFilename">fmrwhy_bids_constructFilename() (in module code)</a>
+      <li><a href="api.html#fmrwhy.bidsutils.fmrwhy_bids_getAnatDerivs">fmrwhy_bids_getAnatDerivs() (in module fmrwhy.bidsutils)</a>
+</li>
+      <li><a href="api.html#fmrwhy.bidsutils.fmrwhy_bids_setupQcDerivDirs">fmrwhy_bids_setupQcDerivDirs() (in module fmrwhy.bidsutils)</a>
+</li>
+      <li><a href="api.html#fmrwhy.bidsutils.fmrwhy_bids_setupQcSubDirs">fmrwhy_bids_setupQcSubDirs() (in module fmrwhy.bidsutils)</a>
+</li>
+      <li><a href="api.html#fmrwhy.settings.fmrwhy_defaults">fmrwhy_defaults() (in module fmrwhy.settings)</a>
+</li>
+      <li><a href="api.html#fmrwhy.settings.fmrwhy_settings_validate">fmrwhy_settings_validate() (in module fmrwhy.settings)</a>
+</li>
+      <li><a href="api.html#fmrwhy.utils.fmrwhy_util_checkDependencies">fmrwhy_util_checkDependencies() (in module fmrwhy.utils)</a>
+</li>
+      <li><a href="api.html#fmrwhy.utils.fmrwhy_util_saveNiftiFrom4D">fmrwhy_util_saveNiftiFrom4D() (in module fmrwhy.utils)</a>
+</li>
+      <li><a href="api.html#fmrwhy.workflows.fmrwhy_workflow_qc">fmrwhy_workflow_qc() (in module fmrwhy.workflows)</a>
+</li>
+      <li><a href="api.html#fmrwhy.workflows.fmrwhy_workflow_qcSubReport">fmrwhy_workflow_qcSubReport() (in module fmrwhy.workflows)</a>
 </li>
   </ul></td>
 </tr></table>