You can use bbregister to compute the transformation for each run based on the middle time point of that run (and assuming you've motion corrected the run), then use mri_vol2surf to resample any data set aligned with the middle time point to the subject's surface or the fsaverage surface. You can do that for each run separately, then use fscalc to compute the difference. doug

francesca strappini wrote:

Sorry, I try to be more specific. I would like to be able to take the volume-to-surface transformation calculated on one set of functional data, and apply that transformation to another set of functional data (the subtraction) of the same subject. This will allow me to display arbitrary functional values on a surface.

Thanks!

Francesca

It was probably the initialization that failed. To test this, run fslregister (very similar command line to bbregister). If that does not look good, then it is an init problem. If these were acquired in the same session, then you can try using --init-header. If you have spm installed, you can try --init-spm. The spm solution requires that SPM be set up properly for this program, which is not always so easy. It also requires matlab.

doug

francesca strappini wrote:

Thanks a lot! I tried the registration with bbregister but unfortunately when I checked the result the functional volume was very distant from the target. Could I tried something else to improve the registration?

I typed:

bbregister --s subject --mov name_file.nii --reg register.dat --init-fsl --bold

Thanks again!

Francesca