Editing Scanco User Instructions (section)

==Draw Contours==
*Contours, or GOBJ files, are drawn to define regions of interest.  Depending on the analysis required, contours may be drawn to isolate the object from the sample tube or to separate bone compartments (e.g., cortical versus trabecular).  
*Contouring is the first step in the analysis process, which allows you to segment the desired bone from surrounding tissues.


===Contouring Tools Reference Sheet===
*[[Media:Contouring-tools.pdf |'''Contouring Tools Reference Sheet''']]
*Contours must always be drawn COUNTER-CLOCKWISE!!!  


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===Contour and Run the Standard Patient Evaluation===
The following instructions are for contouring standard patient radius and tibias. 

#Open the Evaluation Program and select your sample.
#*Refer to [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] for general instructions on how to open the evaluation program and draw a contour.
#Zoom into the desired bone (Radius or Tibia)
#*Using the zoom menu from the top panel, zoom into the Radius or Tibia. 
#*Usually 3x zoom is appropriate.
#Draw contours roughly around the bone.
#*Select the first contouring tool (top left button) and draw COUNTER-CLOCKWISE.
#Automatically generate contours for all slices in the scan.
#*Double click the image to bring up the contouring window. 
#*Double click again and the program will attempt to snap the contour to the bone. Double click again if needed.
#*Select Forwards, and then Iterate Forwards to have the evaluation program automatically segment the bone. 
#Modify any contours as needed.
#*Select the second contouring tool (2nd button from top) to fix any "wrong" contours. 
#*Draw COUNTER-CLOCKWISE!!
#*If many contours cannot be automatically generated correctly i.e. cortical bone is porous and evaluation program misses a lot of bone, it may be better to use the Range/Morph function rather than fixing each individual slice. 
##This is done by first clearing all the breakpoints (Clear all BP in contouring window). The boxes will now become red.
##Manually fix the slice that does not have the correct contour automatically drawn, skip a few slices and manually fix that slice as well. The slices that you have fixed will turn green, indicating that it is a breakpoint (BP). 
##Now you can morph between the two breakpoints (BP, green boxes) you have just created. Select the BP with the higher slice number, select range (first column on left) from the contouring window, followed by morph (second column from left).
#Save Contour (.GOBJ): Make sure you save your work!
#Run the 3D Standard Evaluation for your specific project (and timepoint). 
#*Select 3D evaluation under Tasks to bring up the window. You'll then need to Select... the evaluation specific for your project. 
#*There are a variety of evaluations to choose from, you can search for your project's evaluation script by typing in the name of your project in the filter window. 
#Check the queue to ensure that the evaluation is running properly.
#*Type <code>$ show que</code> in a terminal window will allow you to see all running processes.


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===Correct Trabecular Contours and Run the Cortical Evaluation===
Once the standard evaluation has been completed, an auto-segmentation process is completed to segment the cortical from the trabecular bone. However, the auto-segmentation is not always accurate, and hence the contour (TRAB.GOBJ) will need to be checked.

#Load TRAB.GOBJ by selecting File, then load GOBJ from the top panel.
#*You will now see a list of all GOBJ files pertaining to your sample. You'll need to load the TRAB.GOBJ.
#*When the TRAB.GOBJ has loaded, you will see that the loaded contour is between the cortical and trabecular bone.
#Correct contours as needed
#*Can manually adjust the slices or use the Range/Morph function. 
#*Remember to draw COUNTER-CLOCKWISE!
#Run the 3D cortical evaluation for your specific project (and timepoint, if relevant). 
#*Select 3D evaluation under Tasks to select the appropriate evaluation script. 


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