SUMA Color Display

AFNI Message Board
1

Hello!

I have been using SUMA to show 3d images of white matter tracts. This summer, I was able to open the tracts and they looked very smooth; however, when I try to open the same files now they look blocky. Is there something that I can change to get smooth tracts again?

I’ve attached both images at the below link so that you can see the difference.
SUMA_Issue

Thanks,
Derek Archer

2

How are you making and displaying these volumes? Are you loading them in with ‘-vol …’ or as surfaces made with, for example, IsoSurface?

–pt

3

Hi pt –

These are volumes that were created with IsoSurface. I then load these volumes in with the following command in a script:


Group = TT_N27_plus

        StateDef = smoothwm_plus

NewSurface
        SurfaceFormat = ASCII
        SurfaceType = GIFTI
        SurfaceName = lh.smoothwm.gii
        LocalDomainParent = SAME
        SurfaceState = smoothwm_plus
        EmbedDimension = 3
        Anatomical = Y
        LabelDset =  lh.aparc.a2009s.annot.niml.dset

NewSurface
        SurfaceFormat = ASCII
        SurfaceType = GIFTI
        SurfaceName = rh.smoothwm.gii
        LocalDomainParent = SAME
        SurfaceState = smoothwm_plus
        EmbedDimension = 3
        Anatomical = Y
        LabelDset =  rh.aparc.a2009s.annot.niml.dset

NewSurface
        SurfaceFormat = ASCII
        SurfaceType = Ply
        SurfaceName = name.ply
        LocalDomainParent = SAME
        SurfaceState = smoothwm_plus
        EmbedDimension = 3
        Anatomical = Y

Nothing has changed since the last time I used this script, which is why I’m confused why these files look different now. Is there a setting or something that I may need to change?

4

So, when you overlay the two data sets (“summer” and “winter”), you can see blocky parts in one sticking out of the other?

Is it possible that the SUMA environment file is different now? I wonder if the same underlying blockiness might just look different because the ‘shadowing’ by either “modulation by background intensity” (toggled by hitting the ‘a’ key when the SUMA window is in the selected forefront) and/or the “background colors” (toggled with the ‘b’ key).

To actually change the smoothness of the output mesh, when you run IsoSurface, you can control smoothing of the regions with “-Tsmooth KPB NITER”:


-Tsmooth KPB NITER: Smooth resultant surface using the Taubin smoothing
                         approach in SurfSmooth and with parameters KPB and 
                         NITER. If unsure, try -Tsmooth 0.1 100 for a start.

–pt

5

Hi pt –

Adding the Tsmooth to IsoSurface made it look much better, thanks!

One final question – I usually use the bw20 cmap file for my brains, and am having trouble getting that to show up on the dialog box. Where would this file be located? I’m interested in saving it to my working directory so I can select bw20 by using the “New” button.

Thanks,
Derek

6

Hi Derek,

If you have trouble selecting an entry from a pull-down
menu in afni or suma, right-click on the text to the left
of the menu. That will open up a scrollable popup menu.
For example, right-click over “Cmp” for the colormap
selection menu.

This applies to basically any such menu (that has the
little rectangle on the right side of the menu area, e.g.
just to the right of NN in the “Col” menu, above).

  • rick
7

This is an awesome trick! Thank you guys so much :slight_smile: