Repository: nilearn/nilearn

Issue:
Restructure the section 5 of the docs
Section 5 of the docs is split as follows:

<pre>
5. Image manipulation
5.1. Data preparation: data loading and signal extraction
5.2. Manipulating brain volume: input/output, masking, ROIs, smoothing...
</pre>


The 2 subsections have overlaps, and title that don't summarize what's in them. When teaching, I spend my time jumping from one to the other, which is an indication that it's not structured at all the right way.

Here is how I suggest to restructure:

<pre>
5. Image manipulation
5.1. Input and output: neuroimaging data representation (would integrate current 5.1.1, 5.2.1, 5.2.2)
5.2. Manipulating brain volumes: resampling, filtering, smoothing, masking, ROIs...
5.3. From neuroimaging volumes to data matrices: the masker objects
</pre>


What do people think: @banilo (this may affect how we teach), @AlexandreAbraham, @mrahim, @KamalakerDadi ?



Discussion:
I agree, sounds good to me.


Resolving patch:
diff --git a/doc/conf.py b/doc/conf.py
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -14,7 +14,6 @@
 
 import sys
 import os
-import shutil
 import sphinx
 
 # If extensions (or modules to document with autodoc) are in another
diff --git a/examples/01_plotting/plot_demo_glass_brain_extensive.py b/examples/01_plotting/plot_demo_glass_brain_extensive.py
--- a/examples/01_plotting/plot_demo_glass_brain_extensive.py
+++ b/examples/01_plotting/plot_demo_glass_brain_extensive.py
@@ -60,9 +60,8 @@
                           black_bg=True, display_mode='lzr', threshold=3)
 
 ###############################################################################
-title = 'plot_glass_brain with display_mode="lyrz"'
 plotting.plot_glass_brain(localizer_tmap_filename, threshold=0, colorbar=True,
-                          title='plot_glass_brain with display_mode="lyzr"',
+                          title='plot_glass_brain with display_mode="lyrz"',
                           plot_abs=False, display_mode='lyrz')
 
 plotting.show()
diff --git a/examples/03_connectivity/plot_multi_subject_connectome.py b/examples/03_connectivity/plot_multi_subject_connectome.py
--- a/examples/03_connectivity/plot_multi_subject_connectome.py
+++ b/examples/03_connectivity/plot_multi_subject_connectome.py
@@ -99,19 +99,23 @@ def plot_matrices(cov, prec, title):
 atlas_imgs = image.iter_img(msdl_atlas_dataset.maps)
 atlas_region_coords = [plotting.find_xyz_cut_coords(img) for img in atlas_imgs]
 
-title = "GraphLasso"
-plotting.plot_connectome(-gl.precision_, atlas_region_coords,
-                         edge_threshold='90%',
-                         title="Sparse inverse covariance (GraphLasso)")
 plotting.plot_connectome(gl.covariance_,
                          atlas_region_coords, edge_threshold='90%',
-                         title="Covariance")
-plot_matrices(gl.covariance_, gl.precision_, title)
+                         title="Covariance",
+                         display_mode="lzr")
+plotting.plot_connectome(-gl.precision_, atlas_region_coords,
+                         edge_threshold='90%',
+                         title="Sparse inverse covariance (GraphLasso)",
+                         display_mode="lzr",
+                         edge_vmax=.5, edge_vmin=-.5)
+plot_matrices(gl.covariance_, gl.precision_, "GraphLasso")
 
 title = "GroupSparseCovariance"
 plotting.plot_connectome(-gsc.precisions_[..., 0],
                          atlas_region_coords, edge_threshold='90%',
-                         title=title)
+                         title=title,
+                         display_mode="lzr",
+                         edge_vmax=.5, edge_vmin=-.5)
 plot_matrices(gsc.covariances_[..., 0],
               gsc.precisions_[..., 0], title)
 


Test patch: