How to display spm results on a inflated surface in suma

AFNI Message Board
1

Dear suma users, I just display my spm results on suma:

3dcopy spmt_0001.img.hdr AFNI_spmT
3drefit -view tlrc -space MNI AFNI_spmT+tlrc.
afni -niml &
suma -spec N27_lh.spec -sv MNI_N27+tlrc.

how can I change the underlay surface in to a inflated one, like a freesurfer’s surface?

Thanks a lot!!!

2

Hi-

For viewing purposes, it doesn’t matter where the data set came from, as long as it in the standard space matching your surface.

Probably you want to the hit the comma “,” or period/fullstop “.” to toggle viewing states in SUMA.

For SUMA info, see:
page 12 and following here:
https://afni.nimh.nih.gov/pub/dist/edu/latest/afni_handouts/suma.pdf
which has the accompanying fun “short list” of key strokes:
https://afni.nimh.nih.gov/pub/dist/edu/latest/afni_handouts/suma_keystrokes.txt

and the online documentation of SUMA:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/SUMA/main_toc.html

–pt

3

Dear ptaylor,
Thanks very much for your reply, I use @SUMA_Make_Spec_FS to buid a surface form freesurfer, I used the command like:

@SUMA_Make_Spec_FS filesname -sid Average_surface

Then I got a file containing Average_surface_lh.spec
I want to display the surface in SUMA, and overlay with the spm results. could you tell me how can I open it in SUMA?
Thanks,

Best Wishes，
Irene

4

Hi-

Your commands above should already do this:

Use this to open afni in a directory where the MNI space template is (or you might have it in a directory for “global session” loading), as well as your results you want to view on the surface:


afni -niml &

And put the results you want to view as a surva

Use this to open the “both” *.spec file from your FreeSurferization-- I note now that you might have missed out the important “-niml” above


suma -niml -spec Aver*both.spec -sv MNI_N27+tlrc.

… and while you have the SUMA window selected and the mouse is hovering over it, hit the “t” key, and that should make AFNI & SUMA talk, sending displayable information back-and-forth to each other.

-pt

5

Thanks a lot! it works!
Could you tell me how to get the MNI_N27+tlrc.?
When I tap “t” , it said “Not one of the surfaces is mappable and has a Surface Volumn. Do you sure use the -sv option when launching SUMA”

Best wishes!
Irene

6

The file of MNI surfaces is here:
https://afni.nimh.nih.gov/pub/dist/tgz/suma_MNI_N27.tgz

See one of the earlier posts in this thread for using “-sv *”. You do need it to locate the surface volume for talking between AFNI and SUMA. You can probably use any of the *nii volume files in the suma_MNI_N27/ dir for that.

–pt

7

Thanks so much!! This is really helpful!! It works!
I would like to change the bottom threshold of colorbar for overlay functional data,
So I choose sub-brick of functional dataset in order to change threshold,
but value can’t be changed. like Olay # 0 # 0
could you tell me how to change the bottom value of the color bar?
Thanks so much!

8

The bottom of the color bar maps either to the negative of the range value by default or zero for “Pos only” values. You could of course change the threshold of the dataset, even setting the threshold sub-brick to the the same as the overlay sub-brick volume. Another way is to set the AFNI environment variable, AFNI_PBAR_THREE to YES before starting the afni GUI. That will allow you to drag the sashes at the bottom and top of the overlay color bar, and set how the colors are displayed outside the color bar range by clicking directly on that part of the color bar.

9

Thanks a lot！！ I can change the range of color bar now!!!
How can I change the p-value to T-value for the color bar, and the T-value also shows on the side of color bar?
Best wishes~
Irene