On 9/29/15 3:36 PM, Martin Tisdall wrote:

I am trying to produce a scalar overlay from PET data to overlay onto the pial surface. I have coregistered the pet with T1.mgz and then used the transform from mri_info --scanner2tkr to co-localise with orig.mgz.

What does that mean? You'll need to run bbregister to get the registration file

I then do: mri_vol2surf --src <coregistered pet> --out <output file.w> --out_type paint --regheader <subject> --hemi lh --surf pial --projfrac 0.5.

If you want it on the pial surface use --projfrac 0.0. The way you have it now, it will sample a distance of half the thickness beyond the pial surface. Also, I would recommend using .mgh as the output format as not many tools work the paint files.

The output doesn't seem quite right as seems to be some areas of signal drop out. Can anyone tell me if my options look right or am I missing something. Thank you Martin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer