AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

|
November 20, 2020 06:02PM
Hi-

Yes, to project data from a volume onto a surface, you can use 3dVol2Surf.

How did you create your surface? Did you use FreeSurfer's recon-all and then convert all the output to NIFTI+GIFTI dsets (where standard meshes are created, which are quite useful) with AFNI's @SUMA_Make_Spec_FS?

If you did use those couple of commands, then an example if your ROI is in the right hemisphere (rh) might be:
3dVol2Surf                          \
    -spec std.141.${subj}_rh.spec   \
    -surf_A  std.141.rh.smoothwm.gii \
    -map_func mask                   \
    -sv          DSET_ROI \
    -grid_parent DSET_ROI \
    -out_niml     std.141.rh.ROI_NAME.niml.dset
To view in suma, open your surfaces in SUMA:
suma -onestate -spec std.141.${subj}_both.spec -sv ${subj}_SurfVol.nii
.. then open the Surface Controller, select "Load Dset", (might have to change the list of dsets shown to have *rh* in it), and then view your dset. Is that reasonable?

NB: This video shows some of the visualization options for loading+viewing a dset:
[www.youtube.com]
(as well as drawing one, and other things with the SUMA GUI).

A lot of optionality with the mapping process dependes on:
+ does your ROI intersect clearly with the surface, or just bound on it?
+ are you aiming to project the ROI from being between two surfaces (like the GM-WM border and the pial), or just using one?

But the above is a starting point for mapping an ROI.

--pt
Subject Author Posted

change volume ROI to surface dset

suhyun84 November 20, 2020 05:34PM

Re: change volume ROI to surface dset

ptaylor November 20, 2020 06:02PM