Editing Scanco User Instructions (section)

=== Evaluation ===
The evaluation application on the new system provides the same functionality, but in a different layout. To select which file to evaluate, click <code>File > Load Image from Server</code>. From here, select the project, sample and measurement to populate the associated ISQ file. You may also choose to filter the list of files by [[Scanco_User_Instructions#Scan_Groups| Scan Group]] if you had created one for your samples (Samples) or search by sample name (filter).  

[[File:Load_from_server.png|500px]]

There are three windows: Viewing, Contouring and Tasks.

[[File:eval_tabs.png|400px]]

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==== Viewing ====
To load the slices of your image, click the ‘Load’ button in the bottom right corner. This will start loading any slices after the current viewpoint that have not been loaded yet. Press ‘Cancel’ to stop loading slices from the server. 
The viewing window populates the buttons in the bottom half of the screen from [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|VMS Evaluation]].

[[File:new_viewing_buttons.png|500px]]

These allow you to measure pixel values, distances and view histograms. You can view any of the three planes (XY, XZ, YZ) and scroll through the slices. You can also select the 3D tab, which displays all three planes together. 
The top right corner of the left viewing window has options to hide contours, orientation labels, patient info, colour gradient, slice number, scale bar, or reset orientation.

<code>Tools > Image Header</code> allows you to see the ISQ header information and processing log (if processing has been done on the loaded image).

<code>Options</code> allows you to change the pixel units and colour gradient type. 

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==== Contouring ====

The second window is where you can draw the contours for your evaluation. All of the functionality from contouring in [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|VMS]] is still there, just organized more compactly: 

[[File:contour_buttons.png|500px]]

These new buttons map to the old ones:

[[File:contour_button_mappings.png|500px]]
 
To view what is segmented within the drawn contours (white for bone, blue for non-bone), switch to the [[#Tasks|Tasks]] window and select a script to see its specific thresholding.

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==== Tasks ====
This is the window where you can run your analysis [[Scanco_User_Instructions#Scripting|scripts]], after you have drawn the appropriate contours. By clicking the buttons next to the parameter box (or F5), you can view the segmented parts of the image within the contours.

[[File:segment_show.png]]
  
Some scripts have different segmentation types (for example, trabecular bone with air-hole filling will have a red section for soft tissue, white for bone and black for air).

[[File:segmentation_mask.png|500px]]

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