Using AFNI to co-register two surfaces


I have a NIFTI file that shows how many participants show tuned responses at each location on the cortical surface (figure below).

This NIFTI file is in Talairach space (TT_N27_SurfVol in AFNI). I have mapped this file on std.141.TT_N27_both.spec in AFNI. I want to map the activity from std.141.TT_N27_both.spec on each of my subjects surfaces (std.141). I have created the surface of each subject in FreeSurfer and convert it to AFNI format using @SUMA_Make_Spec_FS. Would you please tell me which command I should use in AFNI to project activity from one surface to another? Is it SurfToSurf? I read about this command that is used to interpolate data from one surface (S2) to another (S1), assuming the surfaces are quite similar in shape but having different meshes (non-isotopic). But here, the two surfaces have a similar mesh (std.141) and different shapes.
After projecting the activity on the subject’s surface, I want to save it as a NIFTI file to use it as an ROI for the analysis. Would you please tell me what the command is for this conversion?

Since you’re already using the standard surfaces (std.*) the surfaces are already co-registered (so to speak… err type). If you had non-standard surfaces or wanted to go from a std surface to another surface you could use SurfToSurf. But there’s really no point - the accuracy of std surfaces across subjects is excellent according to Ziad’s original documentation in SUMA/AFNI.

If you want to go full circle from Surfaces to Volumes you can use 3dSurf2Vol.

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Just to add a bit to Peter’s helpful comment—some of this topic is covered more in the AFNI Academy “Bootcamp” lectures on SUMA, in particular here for this topic:

And this paper describes the concept+development of standard surface meshes:
Argall BD, Saad ZS, Beauchamp MS (2006). Simplified intersubject averaging on the cortical surface using SUMA. Human Brain Mapping 27: 14-27.
Simplified intersubject averaging on the cortical surface using SUMA - PubMed



Thank you for your reply.
I have mapped activity from a nii file on the standard surface (std.141.TT_N27_both.spec) like the figure below. The nii file was in TT_N27_SurfVol.nii space.

I want to map the above activity from std.141.TT_N27_both.spec to the subject surface that is in standard activity, too. As I said in my previous message, I have created each subject’s surface in FreeSurfer and converted it to AFNI format using @SUMA_Make_Spec_FS.
Which command should I use to map the activity from std.141.TT_N27_both.spec to subject’s standard surface?
Actually, what I want is a mask (nii file) of yellow and orange activity. But I want the mask in my subject’s native space.


Just noting that this question has now been asked here on the AFNI Message Board:,166520,166520#msg-166520
and I guess the thread of the discussion will move there.


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… and just to note, a solution with 3dSurf2Vol and 3dVol2Surf has been reached:,166520,166550#msg-166550

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