Hi Hubert, The physical side of the image in fslview is not indicative of the actual side. You have to look at the little letters on the side to see what side it is actually on. When you do this, do you see an R or an L? BTW, you might want to use mris_volsmooth which was written to do this kind of thing. Also, I would not use the .w file format. That format is pretty old and does not support multiple frames. Just use mgh format.

doug

On 12/05/2012 05:40 PM, Fonteijn, H.M.J. (H.) wrote:

Hello,

I'm relatively new to Freesurfer so chances are that this is a pretty basic error on my side but here goes anyhow. I'm trying to use mri_vol2surf for surface-based smoothing of functional MRI data. I would then like to extract time courses from the surface with spm functions by converting the surface to a volume again with mri_surf2vol.

Specifically the commands I'm using are: bbregister --s subject0016 --mov volume0001.nii.gz --reg epi2T1.dat --init-spm --bold mri_vol2surf --mov volume0001.nii.gz --reg epi2T1.dat --surf-fwhm 8 --hemi lh --projdist-avg 0 1 0.1 --o ./volume0001Surf_lh.w --out_type paint mri_surf2vol --surfval volume0001Surf_lh.w paint --hemi lh --projfrac 0.5 --reg epi2T1.dat --o volume0001Surf2Vol_lh.nii --template volume0001.nii.gz

Registration looks allright with tkregister2. I'm only using one volume (volume0001.nii.gz) to test this set of commands. However if I now view volume0001Surf2Vol_lh.nii in fslview, it shows the hemisphere on the right. I'm pretty sure that this is actually the left hemisphere but now flipped. I wonder how this can be solved.

All the best, Hubert _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer