I am attempting to project an ROI (in NIfTI format), which is a collection of about 450 individual coordinates all around the auditory cortex (both hemispheres), to a surface. Unfortunately, when I load the ROI, it shows up as maybe 30 coordinates, still in the correct region, just not nearly as many as when viewed on the volume. If I load the smoothed version of the ROI, it looks completely fine.
I originally loaded the ROI as an overlay in AFNI and projected that onto the surface, but my understanding is that SUMA only reads the colors, not the individual voxel values from the ROI in that method. Could this be what is causing the poor projection? If so, what could I try as a solution? If not, do you have any suggestions for something else I could try to get all my coordinates of interest to show up on the surface?
Thank you so much for your help!
I’m not completely clear as to what you are trying to do. It may be useful to provide some example commands you have tried. To display an ROI in suma, you have some choices.
- Map the ROI volume to the surface with 3dVol2surf.
- Make a surface for the ROI volumes with IsoSurface
- Show the ROI as a volume with “suma -vol myrois.nii”
Sorry for the intensely late response and the vague question.
Here’s what I have:
- surfaces converted from FreeSurfer of the subject’s anatomy
- a NIfTI file with a frequency tuning map (each voxel has a value range 1-8 depending on the frequency it activates most highly to) generated through an SPM analysis
What I would like to do:
- project the tuning map onto the surface in such a way that I can smooth the map after it is in surface space, rather than smoothing in volume space and then projecting it because the volume space smoothing has caused some spacial accuracy issues once on the surface.
I have previously only been using SUMA in conjunction with the AFNI overlay/underlay, using the anatomical as the underlay and the tuning map as the overlay. I have messed around with 3dVol2Surf, but I don’t think I am inputting appropriate data in the grid_parent option.
Any advice is very much appreciated!
It would be useful to give an example of what you tried on the command line and what went wrong. For trying out various parameters with 3dVol2Surf, I recommend the Vol2Surf plugin. That will interactively update the suma display if the two are talking. You will usually need to update the display in some way like changing the threshold or move a slice.
Thanks you, the plugin was good advice. I had seen advice about it elsewhere on the message board, but I am so new to AFNI that I had no clue where to even find the plugins.
I basically have exactly what I want now, just one trivial question. In the object controller of SUMA, is there a way to adjust the intensity scale so that it only displays a positive range as you can do in the AFNI overlay control? I would like to display only 0-8, but every time I adjust the lower threshold of “I,” the upper threshold adjusts to the same number but positive.
E.g. I change the lower threshold to zero and the upper threshold automatically changes to 0. I change it to -1 and the upper threshold updates to 1. And so on.
I’m sure it’s a quick fix, I just couldn’t find anything specifically about it in the object control manual.
Thanks so much for your help!
You can turn off the “auto-symmetrized” intensity in the SUMA controller.
Beneath the grid of values where you are entering Min/Max intensity, and below the “Col” and “Cmp” entries are a few briefly named options with squares to toggle behavior on/off. Unselect the square to the left of “sym I”-- that is what enforces the symmetric ranginess. (To see more details, click on the “BHelp” button at the upper-left of the Control Panel, and then click on that option name again to see the full “button help” about it.
It is the bottom-most item circled in magenta here:
if that helps.
Thanks so much, that was exactly what I needed!