Dear Freesurfer users,
Thank you for your previous help and advice. I am still having difficulty creating reasonable-looking surface overlay files from the functional data in volume format, and would be grateful for any further help.
I have a functional image in volume format (originally written to .nii format, converted with fslchfiletype ANALYZE to .img format), which is a SPM image of MEG activity in particular subject subject1, created with SPM8 MEG analysis software (UCL). I would like to display this activity as a surface overlay on the cortical surface of a different subject, subject2, in tksurfer. I use tkregister2, with --mov as the functional image .img and --s as subject2, to align the two images and create an appropriate register.dat file. When I try to create a surface overlay from the functional image:
mri_vol2surf --mov f.img --out f-rh.img --reg register.dat --hemi rh --surf inflated
- the resulting suface overlay does not correspond well to the activation seen on the original volume image. For example, in the functional volume image viewed in tkmedit on subject1's anatomy, activity which is around the occipital pole (early visual areas) when converted through this method to a surface overlay is now very much anteriorly shifted (i.e occipital-temporal junction). It is the same whether I use .w or .mgh as output file types. I have tried a method avoiding the register.dat file:
mri_vol2surf --mov f.img --out f-rh.img --regheader subject1 --srcsubject subject1 --trgsubject subject2 --hemi rh --surf inflated
- the activity pattern on the surface overlay is almost identical to previous attempt and registration is not improved.
To check whether this was just an inter-subject problem, I created new register.dat file to map the functional volume onto subject1's own cortical surface and repeated mri_vol2surf with --reg register.dat. The activity pattern on the new cortical surface is still very anteriorly shifted in the same way as in the previous attempt in the other subject. Could there be some kind of coordinate mis-alignment between my functional image and the anatomical surfaces? As a novice to these kinds of image manipulations, I can't guess at the solution!
Thanks for your help, Nela