[DOC 📄] api matlab

docs/build/html/genindex.html

@@ -215,15 +215,6 @@ <h2 id="B">B</h2>
       <li><a href="pages/13.01.apireference/generated/enigmatoolbox.plotting.surface_plotting.build_plotter.html#enigmatoolbox.plotting.surface_plotting.build_plotter">build_plotter() (in module enigmatoolbox.plotting.surface_plotting)</a>
 </li>
   </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li>
-    built-in function
-
-      <ul>
-        <li><a href="pages/13.02.apireferencematlab/index.html#ello.byebye">ello.byebye()</a>
-</li>
-      </ul></li>
-  </ul></td>
 </tr></table>
 
 <h2 id="C">C</h2>
@@ -238,13 +229,6 @@ <h2 id="E">E</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li>
-    ello.byebye()
-
-      <ul>
-        <li><a href="pages/13.02.apireferencematlab/index.html#ello.byebye">built-in function</a>
-</li>
-      </ul></li>
-      <li>
     enigmatoolbox.datasets
 
       <ul>
@@ -258,15 +242,15 @@ <h2 id="E">E</h2>
         <li><a href="pages/13.01.apireference/index.html#module-enigmatoolbox.mesh">module</a>
 </li>
       </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li>
     enigmatoolbox.permutation_testing
 
       <ul>
         <li><a href="pages/13.01.apireference/index.html#module-enigmatoolbox.permutation_testing">module</a>
 </li>
       </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li>
     enigmatoolbox.plotting.surface_plotting
 
@@ -300,12 +284,10 @@ <h2 id="L">L</h2>
       <li><a href="pages/13.01.apireference/generated/enigmatoolbox.datasets.load_example_data.html#enigmatoolbox.datasets.load_example_data">load_example_data() (in module enigmatoolbox.datasets)</a>
 </li>
       <li><a href="pages/13.01.apireference/generated/enigmatoolbox.datasets.load_fc.html#enigmatoolbox.datasets.load_fc">load_fc() (in module enigmatoolbox.datasets)</a>
-</li>
-      <li><a href="pages/13.01.apireference/generated/enigmatoolbox.datasets.load_fsa5.html#enigmatoolbox.datasets.load_fsa5">load_fsa5() (in module enigmatoolbox.datasets)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="pages/13.01.apireference/generated/enigmatoolbox.datasets.load_mask.html#enigmatoolbox.datasets.load_mask">load_mask() (in module enigmatoolbox.datasets)</a>
+      <li><a href="pages/13.01.apireference/generated/enigmatoolbox.datasets.load_fsa5.html#enigmatoolbox.datasets.load_fsa5">load_fsa5() (in module enigmatoolbox.datasets)</a>
 </li>
       <li><a href="pages/13.01.apireference/generated/enigmatoolbox.datasets.load_sc.html#enigmatoolbox.datasets.load_sc">load_sc() (in module enigmatoolbox.datasets)</a>
 </li>

docs/pages/13.01.apireference/index.rst

@@ -64,14 +64,12 @@ Gene co-expression data
    enigmatoolbox.datasets.fetch_ahba
    enigmatoolbox.datasets.risk_genes
 
-Surface data
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. autosummary::
-   :template: function.rst
-   :toctree: generated/
-
-   enigmatoolbox.datasets.load_mask
+.. Surface data
+   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+   .. autosummary::
+      :template: function.rst
+      :toctree: generated/
+      enigmatoolbox.datasets.load_mask
 
 Surface templates
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -134,7 +132,7 @@ Spin permutations
    enigmatoolbox.permutation_testing.rotate_parcellation
    enigmatoolbox.permutation_testing.perm_sphere_p
 
-Shuf permutation
+Shuf permutations
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. autosummary::

docs/pages/13.02.apireferencematlab/generated/centroid_extraction_sphere.rst

@@ -0,0 +1,21 @@
+.. _apireferencelist_centroid_extraction_sphere:
+
+.. title:: Matlab API | centroid_extraction_sphere
+
+.. _centroid_extraction_sphere_mat:
+
+centroid_extraction_sphere()
+------------------------------------
+
+**Usage** [`source <>>`_]:
+    .. function:: 
+        centroid_extraction_sphere = centroid_extraction_sphere()
+
+**Description**:
+    ...
+
+**Inputs**:
+    **...** ...
+
+**Outputs**:
+    **...** (*...*) – ...

docs/pages/13.02.apireferencematlab/generated/fetch_ahba.rst

@@ -0,0 +1,22 @@
+.. _apireferencelist_fetch_ahba:
+
+.. title:: Matlab API | fetch_ahba
+
+.. _fetch_ahba_mat:
+
+fetch_ahba()
+------------------------------------
+
+**Usage** [`source <https://github.com/MICA-MNI/ENIGMA/blob/master/matlab/scripts/ahba/fetch_ahba.m>`_]:
+    .. function:: 
+        genes = fetch_ahba();
+
+**Description**:
+    Fetch Allen Human Brain Atlas microarray expression data from all donors and all genes (author: @saratheriver)
+
+**Inputs**:
+    **csvfile** (empty or string) – Path to downloaded csvfile. If empty (default), fetches microarray 
+    expression data from the internet.
+
+**Outputs**:
+    **genes** (*table*) - Gene co-expression data, size = [82 x 15634]

docs/pages/13.02.apireferencematlab/generated/load_conte69.rst

@@ -0,0 +1,21 @@
+.. _apireferencelist_load_conte69:
+
+.. title:: Matlab API | load_conte69
+
+.. _load_conte69_mat:
+
+load_conte69()
+------------------------------------
+
+**Usage** [`source <>>`_]:
+    .. function:: 
+        load_conte69 = load_conte69()
+
+**Description**:
+    ...
+
+**Inputs**:
+    **...** ...
+
+**Outputs**:
+    **...** (*...*) – ...

docs/pages/13.02.apireferencematlab/generated/load_fc.rst

@@ -0,0 +1,21 @@
+.. _apireferencelist_mat_load_fc:
+
+.. title:: Matlab API | load_fc
+
+.. _load_fc_mat:
+
+load_fc()
+------------------------------
+
+**Usage** [`source <https://github.com/MICA-MNI/ENIGMA/blob/master/matlab/scripts/load_connectivity/load_fc.m>`_]:
+    .. function:: 
+        [funcMatrix_ctx, funcLabels_ctx, funcMatrix_sctx, funcLabels_sctx] = load_fc()
+
+**Description:**
+    Load functional connectivity data parcellated using Desikan Killiany (author: @saratheriver)
+
+**Outputs:**
+    - **funcMatrix_ctx** (*double array*) – Cortico-cortical connectivity, size = [68 x 68]
+    - **funcLabels_ctx** (*cell array*) – Cortical labels, size = [1 x 68]
+    - **funcMatrix_sctx** (*double array*) –  Subcortico-cortical connectivity, size = [14 x 68]
+    - **funcLabels_sctx** (*cell array*) – Subcortical labels, size = [1 x 14]

docs/pages/13.02.apireferencematlab/generated/load_fsa5.rst

@@ -0,0 +1,21 @@
+.. _apireferencelist_load_fsa5:
+
+.. title:: Matlab API | load_fsa5
+
+.. _load_fsa5_mat:
+
+load_fsa5()
+------------------------------------
+
+**Usage** [`source <>>`_]:
+    .. function:: 
+        load_fsa5 = load_fsa5()
+
+**Description**:
+    ...
+
+**Inputs**:
+    **...** ...
+
+**Outputs**:
+    **...** (*...*) – ...

docs/pages/13.02.apireferencematlab/generated/load_sc.rst

@@ -0,0 +1,21 @@
+.. _apireferencelist_mat_load_sc:
+
+.. title:: Matlab API | load_sc
+
+.. _load_sc_mat:
+
+load_sc()
+------------------------------
+
+**Usage** [`source <https://github.com/MICA-MNI/ENIGMA/blob/master/matlab/scripts/load_connectivity/load_sc.m>`_]:
+    .. function:: 
+        [strucMatrix_ctx, strucLabels_ctx, strucMatrix_sctx, strucLabels_sctx] = load_sc()
+
+**Description:**
+    Load structural connectivity data parcellated using Desikan Killiany (author: @saratheriver)
+
+**Outputs:**
+    - **strucMatrix_ctx** (*double array*) – Cortico-cortical connectivity, size = [68 x 68]
+    - **strucLabels_ctx** (*cell array*) – Cortical labels, size = [1 x 68]
+    - **strucMatrix_sctx** (*double array*) –  Subcortico-cortical connectivity, size = [14 x 68]
+    - **strucLabels_sctx** (*cell array*) – Subcortical labels, size = [1 x 14]

docs/pages/13.02.apireferencematlab/generated/load_subcortical.rst

@@ -0,0 +1,21 @@
+.. _apireferencelist_load_subcortical:
+
+.. title:: Matlab API | load_subcortical
+
+.. _load_subcortical_mat:
+
+load_subcortical()
+------------------------------------
+
+**Usage** [`source <>>`_]:
+    .. function:: 
+        load_subcortical = load_subcortical()
+
+**Description**:
+    ...
+
+**Inputs**:
+    **...** ...
+
+**Outputs**:
+    **...** (*...*) – ...

docs/pages/13.02.apireferencematlab/generated/load_summary_stats.rst

@@ -15,7 +15,7 @@ load_summary_stats(disorder)
     Outputs summary statistics for a given disorder (author: @saratheriver)
 
 **Inputs**:
-    **disorder** ({'22q', 'adhd', 'asd', 'bipolar', 'depression', 'epilepsy', 'ocd', 'schizophrenia'}) – Disorder name, default is None
+    **disorder** ({'22q', 'adhd', 'asd', 'bipolar', 'depression', 'epilepsy', 'ocd', 'schizophrenia'}) – Disorder name, must pick one.
 
 **Outputs**:
-    - **summary_stats** (*table*) – Available summary statistics
+    **summary_stats** (*table*) – Available summary statistics

docs/pages/13.02.apireferencematlab/generated/parcel_to_surface.rst

@@ -0,0 +1,21 @@
+.. _apireferencelist_parcel_to_surface:
+
+.. title:: Matlab API | parcel_to_surface
+
+.. _parcel_to_surface_mat:
+
+parcel_to_surface()
+------------------------------------
+
+**Usage** [`source <>>`_]:
+    .. function:: 
+        parcel_to_surface = parcel_to_surface()
+
+**Description**:
+    ...
+
+**Inputs**:
+    **...** ...
+
+**Outputs**:
+    **...** (*...*) – ...

docs/pages/13.02.apireferencematlab/generated/perm_sphere_p.rst

@@ -0,0 +1,21 @@
+.. _apireferencelist_perm_sphere_p:
+
+.. title:: Matlab API | perm_sphere_p
+
+.. _perm_sphere_p_mat:
+
+perm_sphere_p()
+------------------------------------
+
+**Usage** [`source <>>`_]:
+    .. function:: 
+        perm_sphere_p = perm_sphere_p()
+
+**Description**:
+    ...
+
+**Inputs**:
+    **...** ...
+
+**Outputs**:
+    **...** (*...*) – ...

docs/pages/13.02.apireferencematlab/generated/plot_cortical.rst

@@ -0,0 +1,21 @@
+.. _apireferencelist_plot_cortical:
+
+.. title:: Matlab API | plot_cortical
+
+.. _plot_cortical_mat:
+
+plot_cortical()
+------------------------------------
+
+**Usage** [`source <>>`_]:
+    .. function:: 
+        plot_cortical = plot_cortical()
+
+**Description**:
+    ...
+
+**Inputs**:
+    **...** ...
+
+**Outputs**:
+    **...** (*...*) – ...

docs/pages/13.02.apireferencematlab/generated/plot_subcortical.rst

@@ -0,0 +1,21 @@
+.. _apireferencelist_plot_subcortical:
+
+.. title:: Matlab API | plot_subcortical
+
+.. _plot_subcortical_mat:
+
+plot_subcortical()
+------------------------------------
+
+**Usage** [`source <>>`_]:
+    .. function:: 
+        plot_subcortical = plot_subcortical()
+
+**Description**:
+    ...
+
+**Inputs**:
+    **...** ...
+
+**Outputs**:
+    **...** (*...*) – ...

docs/pages/13.02.apireferencematlab/generated/reorder_sctx.rst

@@ -0,0 +1,21 @@
+.. _apireferencelist_reorder_sctx:
+
+.. title:: Matlab API | reorder_sctx
+
+.. _reorder_sctx_mat:
+
+reorder_sctx()
+------------------------------------
+
+**Usage** [`source <>>`_]:
+    .. function:: 
+        reorder_sctx = reorder_sctx()
+
+**Description**:
+    ...
+
+**Inputs**:
+    **...** ...
+
+**Outputs**:
+    **...** (*...*) – ...