Re: [Freesurfer] Maps/seed on surafce

Have you verified that the Anat-Func registration in FreeSurfer is correct? You can view it with tkregister-sess.

On 06/16/2016 10:26 AM, Martin Juneja wrote:

Hi Dr. Greve,

I used following command for this:

mkanalysis-sess -analysis LH_XY.surf.lh -surface fsaverage lh -fwhm 5 -notask -taskreg LH_XYZ.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5

-mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 3.

Thanks.

On Wed, Jun 15, 2016 at 3:07 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

what was your mkanalysis-sess command?

On 06/08/2016 02:10 PM, Martin Juneja wrote:
> Dear FreeSurfer and SPM experts,
>
> I am trying to calculate functional connectivity maps using
FreeSurfer
> pipeline:
>
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough.
>
> After defining a seed region on raw anatomical image, I
co-registered
> functional data with anatomical data (as reference) and made
sure that
> the seed is at correct place on both anatomical (top left in
attached
> image) and functional (top right) data. Using SPM, I confirmed
> co-registration was fine.
>
> But after running all the steps of FC, looks like the FC maps
are not
> correct: sig.nii.gz at -fthresh 2 3 (shown at bottom left) because I
> am not getting significant FC at seed location. Here, bottom right
> shows the seed location on surface after I convert the seed to
> fsaverage space (for visualization purpose).
>
> Any thoughts, ideas or tips on what went wrong here, would be really
> appreciated.
>
> Thanks.
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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