Merge pull request #29 from DelinteNicolas/doc

Doc
DelinteNicolas · Apr 11, 2023 · 07e7263 · 07e7263
2 parents a5fb576 + 37f8b8a
commit 07e7263
Show file tree

Hide file tree

Showing 5 changed files with 51 additions and 1 deletion.
diff --git a/docs/api.rst b/docs/api.rst
@@ -32,3 +32,12 @@ utils
    :members:
    :undoc-members:
    :show-inheritance:
+
+viz
+^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: unravel.viz
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
diff --git a/docs/imgs/rgb3.webp b/docs/imgs/rgb3.webp
diff --git a/docs/imgs/stream.png b/docs/imgs/stream.png
diff --git a/docs/index.rst b/docs/index.rst
@@ -6,10 +6,18 @@
 Welcome to UNRAVEL's documentation!
 ================================
 
-Welcome to the documentation of Tractography Informed Multi-fascicle microstructure Estimation!
+Welcome to the documentation of UtiliziNg tRActography to uncoVEr muLti-fixel microstructure (UNRAVEL)!
 
 The code is available at https://github.com/DelinteNicolas/UNRAVEL
 
+To unravel has two meanings :
+
+- to disentangle the fibers of
+- to resolve the intricacy, complexity, or obscurity of
+With the UNRAVEL framework, we utilize tractography to unravel the microstructure of multi-fixel models.
+
+This repository contains the documentation of the code used to combine macroscopic tractography information with microscopic multi-fixel model estimates in order to improve the accuracy in the estimation of the microstructural properties of neural fibers in a specified tract.
+
 .. toctree::
    :caption: Getting Started
 

diff --git a/docs/tutorials.rst b/docs/tutorials.rst
@@ -14,6 +14,8 @@ Fixel weights maps can be obtained using the :meth:`unravel.core.get_fixel_weigh
 	t1 = nib.load("peak_file_1.nii.gz").get_fdata()
 
 	trk = load_tractogram("trk_file.trk", 'same')
+	trk.to_vox()
+	trk.to_corner()
 
 	fixel_weights,_,_ = get_fixel_weight(trk, [t0, t1])
 
@@ -27,4 +29,35 @@ A complete example code of the main functions is available in the :class:`unrave
     :language: python
     :lines: 13-
 
+Adding color to streamline trajectory
+-------------------------------------
+
+The `color` parameter can be set to `True` to add directional colors::
+
+	plot_streamline_trajectory(trk, resolution_increase=2,
+						streamline_number=500, axis=1,
+						color=True, norm_all_voxels=True)
+
+.. image:: imgs/stream.png
+	:width: 800
+	:align: center
+
+Create GIFs from 3D volumes
+---------------------------
+
+Short videos can be created using the :meth:`unravel.viz.convert_to_gif` function::
+
+	import nibabel as nib
+
+	rgb = get_streamline_density(trk, resolution_increase = 4, color = True)
+	t1 = nib.load('path_to/registered_T1.nii.gz').get_fdata()
+
+	# rgb = overlap_volumes([rgb, t1], order=0)
+
+	convert_to_gif(rgb, output_folder='output/path', transparency=True, keep_frames=False,extension='gif', axis=0)
+
+.. image:: imgs/rgb3.webp
+	:width: 600
+	:align: center
+
 .. note::  More tutorials will be added in the near future.