Visualizing results - MRIcroS

Owned by Paul Macey (admin)
Last updated: Aug 23, 2016
2 min read

Make sure you have updated all the matlab files, not just CSPM or SPM12, since MRIcroS is in the ...\matlab\mricros subfolder.

Start the GUI:

First step: show the shape (refer to Fig. 1)

  1. Select the mask file; say Yes to create filled mask
  2. Deselect Overlay 1 and 2, click Display

Overlays

Select the file to overlay

For increasing/decreasing, you can select separate files and use different colormaps

To get range of values, use the CSPM function Image intensity info (or type im_info at the command prompt)

This will display min, max and so on, so you can optionally set these so that the color scale is fixed. 

Note that you may need to set the minimum threshold to just over 0, as otherwise everything might be colored with the Overlay.

Save images at fixed intervals

Display the VOI and overlays; to manually rotate with the mouse, make sure "Rotate 3D" is toggled on.

After you have found a good angle, set the view where you want it at a known angle. To set an angle after display, use the "View" command. For example, to set the view at azimuth of 90 and elevation of 45:

>>view (90, 45)

Tip: to get the current view settings, use "view" to two output arguments and no input arguments:

>>[az,el] = view

Edit the CSPM file shape_makeviews: 

>>edit shape_makeviews

See Fig. 2 (right).

  1. Change the "step" to the number of degrees you want to rotate the figure. Example shows setting for 45 degree steps.
  2. Set the folder to save the images. Example will save in D:\temp\Winter. (Put backslash at end in file.)
  3. Select rotation about vertical or horizontal axis; comment out (with "%" symbol) the one you don't want.
  4. Save
  5. Run

Videos

Edit the CSPM file shape_video

>>edit shape_video

 

 

Figure 1

Figure 2: shape_makeviews settings