/**

\page Usage Interaction Details

CapTk always assumes the multi-modal data is coregistered and in the LPS coordinate system. This constraint will be removed in a future release, where it will detect unregistered images and do a basic affine registration while at the same time doing the conversion from RAS to LPS coordinate system.

## Image Loading

Currently, CapTk supports NIfTI (extensions <b>.nii.gz</b>, <b>.nii</b>) and DICOM (extension <b>.dcm</b>) images with the following types of MRI modalities:

-# T1
-# T2
-# T1CE
-# FLAIR
-# Perfusion
-# DTI (non-visualization)

All the file types are loaded from the <b>File -> Load</b> menu. 

\image html 1_loading.png
\image latex 1_loading.png

Various basic operations such as adjusting contrast and brightness (right mouse button click + horizontal/vertical drag on the visualization pane), window and level set (bottom panel) are available for the user. The bottom panel also shows basic information about the image and the currently selected coordinate.

## Tab Docking

Double clicking on the tab bar will dock/undock the entire section (highlighted in red). This behaviour is replicated by single click of the dock/undock button (highlighted in yellow).

\image html 2_dock.png
\image latex 2_dock.png

## Initializing Seed Points

Undernearth the <b>Seed Points</b> tab, there are broadly two types of initializations - tumor points and tissue points. The controls to add/remove points are the same as above. The assigned radio buttons control their selection and related functionality.

\image html 3_seeds.png
\image latex 3_seeds.png

### Tumor Points

These are basically seed points that have a coordinate and a radius. These are helpful for applications like tumor growth model simulation. The controls are as follows:

<table border="0">
  <tr><th>Key Stroke <th>Function
  <tr><td align="center" width="100px">Shift + Space <td align="center">Set initial tumor center
  <tr><td align="center">Ctrl + Space <td align="center">Update tumor radius
  <tr><td align="center">Space <td align="center">Update tumor center
</table>

### Tissue Points

These are basically seed points with just coordinate information. They can be used for a multitude of applications where manual initialization(s) are required for a semi-automated algorithm. There are various tissues that can be initialized in this panel:

<table border="0">
  <tr><th>Tissue Acronym <th>Full Form
  <tr><td align="center">CSF <td align="center">Cerebrospinal Fluid
  <tr><td align="center">VT <td align="center">Ventricular Cerebrospinal Fluid
  <tr><td align="center">GM <td align="center">Gray Matter
  <tr><td align="center">WM <td align="center">White Matter
  <tr><td align="center">VS <td align="center">Vessels
  <tr><td align="center">ED <td align="center">Edema
  <tr><td align="center">NCR <td align="center">Necrosis
  <tr><td align="center">TU <td align="center">Enhancing Tumor
  <tr><td align="center">NE <td align="center">Non-Enhancing Tumor
  <tr><td align="center">CB <td align="center">Cerebellum
  <tr><td align="center">CAE <td align="center">Enhancing Cavity
  <tr><td align="center">CAN <td align="center">Non-Enhancing Cavity
  <tr><td align="center">RTN <td align="center">Tumor Recurrence
  <tr><td align="center">RTE <td align="center">Enhanced Tumor Recurrence
</table>

There are some application-specific tissue types, which are enabled when the application is selected and the rest and disabled. For example, when trying to initialize tissue points for GLISTR, only CSF, GM, WM, VS, ED, NCR, TU, NE and CB buttons will be enabled and the rest will be disabled. If there are some required tissue types missing for an application, CapTk will throw a warning and not let the user save the incorrect tissue points. Loading and saving is done via text files in a format consistent with similar applications. This functionality is needed for the following applications (and all derivatives): <a href="https://www.cbica.upenn.edu/sbia/software/glistr/">GLISTR</a>, GLISTRBoost (BRATS 2015 Winning Algorithm) and <a href="https://www.cbica.upenn.edu/sbia/software/portr/">PORTR</a>.

## Drawing Regions of Interest (ROI)

ROIs are useful for applications that need a mask as input. There are the following controls underneath the <b>Drawing</b> tab:

<table border="0">
  <tr><th>Buttons <th>Description
  <tr><td align="center" width="15%">View Mode <td>Switch from drawing mode (which is enabled when either Near or Far ROI drawing is selected) to normal viewing mode
  <tr><td align="center">Marker Size <td>A square marker of specific voxel size. Acts as size for Near and Far ROIs and for eraser
  <tr><td align="center">Near ROI <td>Highlighted in Red and saved as value <b>150</b> in the 0-255 space
  <tr><td align="center">Far ROI <td>Highlighted in Green and saved as value <b>255</b> in the 0-255 space
  <tr><td align="center">Erase Voxels <td>This acts as an eraser for both Near and Far ROIs
  <tr><td align="center">Clear <td>Separate buttons to clear Near and Far ROIs
  <tr><td align="center">Undo <td>Undos last drawing action
</table>

In a future release, we will have an option to select multiple "labels", going up to <b>5</b> different regions of interest per image.

A lot of these usage related documentation is present under the <b>Help</b> menu.
*/
