That looks ok, but if you want to do a group analysis, you can add
--trgsubject fsaverage and the output surface will be in fsaverage
space. You can then concatenate the data together (mri_concat) into one
stack and then run mri_glmfit etc for your group analysis. You may or
may not want to smooth on the surface (mri_surf2surf) as the PET will
already be smooth (unless you did PVC).
On 03/22/2016 01:04 PM, Elijah Mak wrote:
> Hi Freesurfer Community,
>
> I am trying to run a vertex-wise analyses of PET data.
>
> I have already performed bbregister. Next, I did mri_vol2surf for each
> subject, left and right hemispheres.
>
> for i in `cat subjects`; do mri_vol2surf --src
> FS6_${i}_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz --out
> FS6_${i}_MPRAGE_Neuro.nii/surf/lh.PETSurface.mgh --hemi lh --regheader
> FS6_${i}_MPRAGE_Neuro.nii --projfrac 0.5 --interp nearest; done
>
> Is this command correct? Visual inspection on freeview looks OK.
>
> How may I derive the group average from these individual surfaces and
> perform the mri_glmfit?
>
> Any help will be greatly appreciated.
>
> Best Wishes,
> Eli
>
>
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