This page is very incomplete, and unfortunately there isn’t that much documentation elsewhere. So if you know any Display tricks, please add them!
There is a partial user guide on this page: http://www.bic.mni.mcgill.ca/software/Display/Display.html
Frequently Asked Questions
How do I create a 3D rendering of a label?
Open the label in Display. Click somewhere on the part of the label that you want to render in 3D. Go to the “Create Surface” menu (G). Select “Label Bin-Isosurface” (G). Then, in the terminal, type the min and max of the label - for example, if your value is 1, type 0.5 1.5. This should do a marching cubes rendering of the label in the objects window.
How do I crop a volume?
- Start display with your volume to crop as input: Display volume_to_crop.mnc
- Then press on: H - Volume cropping F - Set Crop Source (Enter file name in terminal window) S - Pick Crop Box
- A green contour will appear around the MR planes. y/ou can move the side of this crop window with yoru mouse.
- Save new cropped volume by pressing on: R - Crop to file (Enter file name in terminal window)
How do I superimpose the peaks of a T-map on an anatomical image?
Do Display anatomical.mnc tstat.mnc (this makes your current volume to be tstat.mnc, using the color bar to left-adjust it to your desired threshold value.)
On the main menu click on “color coding” and choose “spectral”. in this same menu you have to make your current volume (i.e. the thresholded tstat.mnc) transparent. To do so, click on “over” or “under” (by default they are set to BLACK and WHITE) and then in the console type “transparent”. Now you should see the anatomical.
If you need to adjust the intensity of the anatomical image, press “pop” and go back to the main menu.
Click on “slice view”. You will see that “curr volume” is set to 2. Just click on it and it will change your current volume to 1, which is your anatomical one. now you can adjust the intensity using the bar on the left.
For other tips on Display, look at http://www.bic.mni.mcgill.ca/users/kate/Howto/Display.html
You may use ray_trace to make complex representation of your results. There is a tutorial provided by David McDonald: http://www.bic.mni.mcgill.ca/users/david/Ray_trace/ray_trace_tutorial.html And here are some extra features: (bold options are those not listed in the help menu. Claude Lepage has kindly suggested to upgrade ray_trace and to release a new version with th next quarantine after CIVET7.0, maybe)
Show positive and negative statistic maps on the entire brain surface.
ray_trace -output outfile.rgb -light -usercc cold_map.txt −13 −6 BOLD_contrast_t.mnc 0 1 -under transparent -over transparent -hot 6 11 BOLD_contrast_t.mnc 0 1 -over transparent -under transparent midsurface.obj -size 400 400 -bg black -crop -bottom
your cold_map.txt file would contain: (you can play with rgb values and generate different maps)
0.00 0.0 0.0 0.0
0.25 0.0 0.0 0.5
0.50 0.0 0.5 1.0
0.75 0.5 1.0 1.0
1.00 1.0 1.0 1.0
(you can use -bottom, -top, -left, -right to set the view.)
show markers, corresponding to activation peaks of different subjects on your brain object
ray_trace -output output.rgb -light -marker_size 3 -marker_colour red subject1_peaks.tag -light -marker_size 2 -marker_colour blue subject2_peaks.tag -light -marker_size 2 -marker_colour subject3_peaks.tag average_midsurface.obj -size 500 500 -bg black -bottom
show subcortical peaks on a subcortical object within a brain object
ray_trace -output output.rgb -light -marker_size 3 -marker_colour red subcortical_peaks.tag average_midsurface_transparent.obj subcortical.obj -size 500 500 -bg black -bottom
to make a transparent object:
change the surface opacity
set_object_opacity average_midsurface.obj average_midsurface_transparent.obj 0.05
or make a wiregrid object
polygons_to_lines average_midsurface.obj midsurface_lines.obj
if you use ray_trace with slice objects (as mentioned in David’s tutorial), make sure your tag file does not have coordinates that are not in the slice plane. That will result in a skewed image.
If you are using multiple surface objects you may need to use -one_hit option with ray_trace