add document for misc tools and screenshot dialog;

brainnetome · Feb 25, 2016 · a6749e5 · a6749e5
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Showing 9 changed files with 61 additions and 10 deletions.
diff --git a/source/download.rst b/source/download.rst
@@ -13,8 +13,8 @@ Download Links
 .. |winlogo| image:: images/winlogo.jpg
 .. |rellogo| image:: images/rellogo.jpg
 
-Current Release (v1.1-r160204)
------------------------------
+Latest Release (v1.1-r160204)
+------------------------------
 
 |winlogo| `Windows Installer (x86-64) 
 <http://diffusion.brainnetome.org/release/DiffusionKitSetup-WIN64-v1.1-r160204.exe>`_

diff --git a/source/frontend.rst b/source/frontend.rst
@@ -61,8 +61,8 @@ so that one can adjust the threshold to get smaller/larger brain outline estimat
 Details on the implement can be found at 
 `BET's UserGuide <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET/UserGuide>`_.
 
-GUI for Diffusion Model Reconstruction
-======================================
+Diffusion Model Reconstruction
+==============================
 
 Starting from this section, we provide three different approaches for diffusion MR data processing:
 
@@ -120,4 +120,38 @@ into multiple ROI files.
 To generate whole brain fiber, just use the brain mask image generated during :ref:`Skull_Stripping`
 as seed input. This may cost a few minutes when HARDI is used as input diffusion model.
 
+Miscellaneous Tools
+===================
+
+Image Registration
+------------------
+
+This is basically the GUI front-end of NiftyReg, while we perform :code:`reg_aladin` 
+on intra-subject images, and addtionally run :code:`reg_f3d` for inter-subject cases.
+
+The details of the tool is described in 
+`Image Registration <userguide.html#image-registration>`_ section in UserGuide page.
+
+.. figure:: images/gui_registration.png
+  :width: 400px
+  :align: center
+
+Create ROI
+----------
+
+The details of the tool is described in `Image calculation and ROI generation <userguide.html#image-calculation-and-roi-generation>`_ section in UserGuide page.
+
+.. figure:: images/gui_createroi.png
+  :width: 600px
+  :align: center
+
+Fiber Pruning
+-------------
+
+The details of the tool is described in `Fiber manipulation <userguide.html#fiber-manipulation>`_ section in UserGuide page.
+
+.. figure:: images/gui_fiberpruning.png
+  :width: 450px
+  :align: center
+
 .. include:: common.txt
diff --git a/source/images/gui_createroi.png b/source/images/gui_createroi.png
diff --git a/source/images/gui_fiberpruning.png b/source/images/gui_fiberpruning.png
diff --git a/source/images/gui_registration.png b/source/images/gui_registration.png
diff --git a/source/images/view_screenshot.png b/source/images/view_screenshot.png
diff --git a/source/index.rst b/source/index.rst
@@ -14,7 +14,7 @@ Homepage
 ========
 
 Welcome to Brainnetome DiffusionKit's Homepage
------------------------------------------------
+----------------------------------------------
 
 .. note:: 
  * a full pipeline for (pre-)processing and visualization for diffusion MRI data.
@@ -36,15 +36,15 @@ Chris Rorden `[4] <reference.html#id4>`_ and the constrained spherical deconvolu
 HARDI reconstruction in MRtrix `[5] <reference.html#id5>`_, 
 were adopted with improved interface and user experience.
 
-For new users, and/or for an overview of DiffusionKit’s basic functionality, 
-please see the `Tutorial <tutorial.html>`_. 
-The rest of the documentation will assume you’re at least passingly familiar with the 
-material contained within.
+* Visit `Manual <document.html>`_ page for a complete list of usage instructions.
+* Visit `Tutorial <tutorial.html>`_ page to take a look at how DiffusionKit can solve your practical problems.
+* Visit `Screenshot <screenshot>`_ page to see how the GUI front-end looks like.
+* For additional problems, please feel free to email us at [email protected] .
 
 *Please see the navigation sidebar to the left to begin.*
 
 .. toctree::
-   :maxdepth: 1
+   :maxdepth: 2
    :hidden:
 
    document.rst

diff --git a/source/screenshot.rst b/source/screenshot.rst
@@ -7,10 +7,16 @@
 Screenshots
 ===========
 
+Tensor and ODF/FOD Visualization
+--------------------------------
+
 |sticks| |slices|
 
 |4A| |mainwindow| 
 
+Tractography Visualization
+--------------------------
+
 |fibers| |fibers2|
 
 .. include:: common.txt

diff --git a/source/visualization.rst b/source/visualization.rst
@@ -75,9 +75,20 @@ in order to spare right mouse click to popup option menu for more actions.
 The background color for 3D view is defined as black by default.
 This can be changed from context menu popped up when *right* mouse click event is captured. 
 By selecting the color from the popup color dialog, the background color is changed instantly.
+
 Also, saving screenshots as PNG image is enabled from the context menu.
 The default image is named after current timestamp to avoid naming duplication.
 
+.. figure:: images/view_screenshot.png
+   :width: 300
+   :align: center
+
+To customize generated image for different requirements, two additional options are
+provided, as shown in the above screenshot. 
+The higher magnification value indicate higher resolution of generated image.
+By enabling transparent background in output image, one can alternate the 
+background color in a later stage.
+
 2D Navigation
 -------------