On 7/10/2021 12:47 AM, Erik Jahner wrote:
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>
> I am interested in obtaining the average intensity within a label from each
> frame of a functional image that has been smoothed on the surface (I have
> generated the label). However, the functional connectivity pipeline seems to
> use only volume based seeds. It seems to me that in using the FreeSurfer
> software we would want to take advantage of the surface based smoothing and
> not return to getting the average of voxels in aparc+aseg.
>
> (1) Am I incorrect in my thinking here?
Yes. If you are going to average within an ROI, there is no need to
smooth. In fact, it can be counter productive as is smears one ROI into
another.
>
> (2) Is there a way to get the mean intensity of a label (I have created) at
> each frame along the surface to get a timcourse for a particular region?
Yes, mri_segstats. Use the --slabel option with --excludeid 0 and
specify the --avgwf option for the output. Spec your surface-sampled
fmri as the input --i
>
> I see there is a way to do this with anatomical features such as thickness,
> but I do not see a way to do this with functional data across frames for
> signal intensity.
>
> Thanks
> ~Erik Jahner
>
>
>
>
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