Re: [Freesurfer] rs-fMRI data on pial surface

Rene, when you specify --projfrac-avg 0 1 .05 is averages over the whole ribbon. Run mri_vol2surf with --help to get more info on what projfrac-avg does doug On 05/15/2013 04:58 AM, René Besseling wrote:

Hi Doug, I'd like the average over the ribbon, so I changed "pial" to "white". I'd think this actually results in a projection of the white surface, but I guess this actually doesn't matter since each white vertex is associated to a directly overlying pial vertex? Best regards,

René

On Tue, May 14, 2013 at 5:48 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Hi Rene, do you want it on the pial surface or the average over the
ribbon? If the pial surface, then use your cmd below but use
--projfrac
0. If you want the average use your cmd below but change pial to white
(or don't spec --surf)
doug


On 05/14/2013 08:00 AM, René Besseling wrote:
> Hi Freesurfers,
> For this analysis I plan to do, I want to map resting-state data in
> native (T1) space to the pial surface. The command I use for
this is:
> mri_vol2surf --src fMRI_nat.nii --regheader subjID --hemi lh
> --projfrac-avg 0 1 0.05 --surf pial --o fMRI_2surf.mgh
> So the intention is to average the resting state data over the
cortex
> and to map this to the pial surface. However, if I'm not
mistaken the
> --projfrac-avg option projects along the outward pointing surface
> normal. Therefore, when using the pial surface, I expected that the
> proper call would be --projfrac-avg 0 -1 -0.05. However, this
command
> does not run, whereas the command given above does, and yields
> (sensible) output. So is the command given above correct after all?
> And does this imply that for the pial surface, the volumetric
data is
> actually projected along the inward pointing normals?
> Best regards,
>
> René
>
>
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