/**

\page Usage Usage

In order to showcase the usage of the PHI Estimator (PHI-E), we will use an example to calculate the PHI for a given subject. Firstly, we run the PHI Estimator and load either NIFTI or DICOM images using <strong>File -> Load -> MRI (NIFTI)</strong>/(or MRI (DICOM)) menu. 

<strong>The PHI Estimator assumes that the input NIFTI images are already co-registered. In case of DICOM images, PHI Estimator co-registers all images before they are displayed. </strong>

PHI Estimator needs at least two images to start calculating the PHI index. These should be one contrast-enhanced T1-weighted (T1-CE) and one Dynamic Susceptibility Contrast (DSC) MRI images. The T1-CE image is displayed, whereas the DSC image is loaded in the background. Users can interact with the T1-CE modality to draw the required Near and Far regions of interest (ROIs). Users can also load a T2-weighted fluid-attenuated inversion recovery (T2-FLAIR) image to aid in the drawing process of the far ROI.

<center>
\image html 1.png "Figure 1: The 'Images' panel of PHI Estimator"
\image latex 1.png "The 'Images' panel of PHI Estimator" width=15cm
</center>

Figure 1 (above), shows an example screenshot of the images panel (a) after loading three MRI images, i.e. T1-CE, T2-FLAIR and DSC image. T1-CE and T2-FLAIR images are displayed in the ‘visualization input images’ panel (b). The DSC image is displayed in the non-visualization input images’ panel (c), and it is stored on the backend for the calculation of the PHI index on the drawn regions. Both the panels show the list of the filenames of the loaded images and their image type, such as T1CE for T1-CE. Users can select which image is shown in the visualization windows (f), (g), and (h) by selecting an image from the panel (b). The visualization windows (f), (g), and (h) show the axial, coronal, and sagittal views of the selected image, respectively. Users can unload individual images by clicking the "X"  button on the left of each image filename. Panel (e) shows a duplication of the list of the loaded filenames for overlay purposes. The "Overlay" tick-box (d) allows for observation of intensity changes from one image to another using a slider. Once this tick-box is enabled, the user must select one image from the top list (b) and another image from the bottom list (e) of images, which will correspond to the images on the left and the right side of the slider (d), respectively. The weight of overlay between the two images is controlled by the slider. The "Preset" (k) and the rest of the controls in the bottom right side of the panel, change the color mapping of the visualization windows, in order to depict different properties of the displayed images. Finally, more detailed image information is shown in (i) panel, and the (j) panel shows the coordinates of the current selected voxel of the image.

Secondly, we need to draw the Near and Far ROIs on the displayed images, i.e. T1-CE and T2-FLAIR. For drawing, the user needs to switch to the ‘Drawing panel’ depicted by (l) in Figure 2. The left most section of this panel is for switching to 'view mode' from the 'drawing mode'. The middle section is for drawing the Near and Far ROIs, whereas the right most section is for clearing the input of each ROI. The drawn Near and Far ROIs can be saved from the menu 'File -> Save -> ROI (NIFTI)'. If Near and Far ROIs already exist, they can be loaded from the menu 'File -> Load -> ROI (NIFTI)'. 


<center>
\image html 2.png "Figure 2: The 'Drawing' panel of the PHI Estimator (Near and Far ROIs)"
\image latex 2.png "The 'Drawing' panel of the PHI Estimator (Near and Far ROIs)" width=15cm
</center>

There are many buttons in this panel, which are briefly described in the following text. 

<table border="0">
	<tr>
        <td width="30%"><strong>Button</strong></td>
	<td width="70%"><strong>Explanation</strong></td>
	</tr>
		</tr>
	<tr><td>View Mode</td>
	<td>Turns the system from drawing mode to the view mode. </td>
	</tr>
  
  <tr>
        <td>Draw Near ROI</td>
	<td>Turns the system to drawing mode if it is in view mode, and enables the drawing of the Near ROI, shown in red (n) in Figure 2. </td>
	</tr>
	<tr><td>Draw Far ROI</td>
	<td>Turns the system to drawing mode if it is in view mode, and enables the drawing of the Far ROI, shown in green (o) in Figure 2.</td>
	<tr><td>Erase individual voxels</td>
	<td>Turns the system to erasing mode, allowing the user to erase individual voxels from the Near and/or the Far ROI.</td>
	</tr>
	<tr><td>Size</td>
	<td>Allows the user to select the size of the marker used both for Drawing or Erasing individual voxels from the Near/Far ROIs.</td>
	</tr>
  
  <tr><td>Clear Near Drawing</td>
	<td>Clears the Near ROI from all slices. </td>
	</tr>
	<tr><td>Clear Far Drawing</td>
	<td>Clears the Far ROI from all slices.</td>
	</tr>
</table>

The user needs to launch the PHI estimation process by using the menu option: <strong>‘EGFRvIII -> Estimate PHI'</strong>. A progress bar appears that shows the progress for the estimation of the PHI index. After the successful estimation, a pop-up window shows the results of PHI estimation.

<center>
\image html 3.png "Figure 3: PHI results window"
\image latex 3.png "PHI results window" width=8cm height=6cm
</center>

The following Table describes various quantitative measures displayed on the pop-up in detail. 

<table border="0">
	<tr>
        <td width="30%"><strong>Button</strong></td>
	<td width="70%"><strong>Explanation</strong></td>
	</tr>
	<tr><td>PHI Index</td>
	<td>The quantitative value for PHI. </td>
	</tr>
	<tr><td>Near/Far perfusion drop ratio</td>
	<td>The ratio of the maximum drop in the temporal perfusion dynamic signals between the voxels of the Near ROI over the Far ROI.</td>
	<tr><td>Near ROI voxels used</td>
	<td>The number of voxels of the Near ROI that had actual perfusion data in the corresponding DSC image (and therefore involved in the estimation of the PHI index), over the number of voxels drawn by the user.</td>
	</tr>
	<tr><td>Far ROI voxels used</td>
	<td>The number of voxels of the Far ROI that had actual perfusion data in the corresponding DSC image (and therefore involved in the estimation of the PHI index), over the number of voxels drawn by the user.</td>
	</tr>
</table>

<strong> Note: The system itself recognizes T1-CE, T2 FLAIR and DSC MRI files based on their filenames. For a file to be identified as T1-CE, it should contain any of these strings (T1CE, t1-ce, T1-CE, t1c, T1C, T1c) as part of any other characters in the filename. Similarly, for a file to be recognized as Flair and DSC, they should contain the (FLAIR, flair, Flair) and (Perfusion, PERFUSION, perf, perfusion) strings in their filenames, respectively.</strong>

The following table describes some of the keyboard and mouse controls. 
<table border="0">
	<tr><td width="30%"><strong>Keyboard controls</strong></td></tr>
	<tr><td width="30%"><strong>Mode</strong></td><td width="70%"><strong>Description</strong></td></tr>
	<tr><td>Viewing Use</td>
	<td>1-4: Change view among loaded images<br>h: Display/Hide Crosshair<br>r: Reset Geometric Adjustments<br>a: Reset Intensity Adjustments</td>
	</tr>
  
	<tr><td>Drawing Mode</td>
	<td>e: Enable/Disable erase mode<br>
      1-9: Change brush size<br>
      Esc: Quit drawing mode </td>
      </tr>

  <tr><td width="30%"><strong>Mouse controls</strong></td></tr>
  <tr><td width="30%"><strong>Mode</strong></td><td width="70%"><strong>Description</strong></td></tr>
  <tr><td>Viewing Use</td>
	<td>U/D: Change slice number<br>
  LB + movement: Move crosshair <br></td></tr>
  
  <tr><td>Geometric Adjustments</td>
  <td>Ctrl + U/D: Zoom in/out (Adjust scaling factor) <br>
 	Ctrl + LB + movement: Pan images (Adjust image's center) 
  </td></tr>
  </table>
  
  <strong> U/D: Up/Down Wheel Scrolling, LB = Left Button, RB = Right Button
  

*/
