Hi Freesurfers,
Thank you for the help you provide through this list.
Is there a way to get, for each vertex, the identify (or thickness values) of the surrounding vertices in a 10mm radius? The command mris_convert has the '-v' option, but that produces only 5-6 vertices and there is no option to query a particular radius.
I imagine this can be done manually outside Freesurfer by first identifying the neighbors for each vertex based on the coordinates, then getting the respective thickness value, but I wanted to check whether there is any easier way or any advice on how to proceed.
Dorian
You can smooth it. This would give you a gaussian kernel instead of the box kernel that you describe. Set the fwhm to the radius you want (mris_fwhm with --smoothonly option)
On 01/31/2017 04:48 PM, Dorian P. wrote:
Hi Freesurfers,
Thank you for the help you provide through this list.
Is there a way to get, for each vertex, the identify (or thickness values) of the surrounding vertices in a 10mm radius? The command mris_convert has the '-v' option, but that produces only 5-6 vertices and there is no option to query a particular radius.
I imagine this can be done manually outside Freesurfer by first identifying the neighbors for each vertex based on the coordinates, then getting the respective thickness value, but I wanted to check whether there is any easier way or any advice on how to proceed.
Dorian
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Douglas, thank you for the quick reply.
I am trying to figure out how can mri_fwhm help in this contect but can't grasp it. I tried some of the example commands in the wiki, applied on a XX.thickness file, but the outcome is NaN.
To clarify, what I am trying to do is detect local variations in thickness which might be a biomarker of pathology. A generic value for the whole brain does not help, I will need to localize the "anomaly". I thought I can do this by something like raw neighboring values, but maybe an estimation of the smoothing of thethickness surface might do the trick. I just can't find out how to compute it (sorry, not an experienced user of freesurfer). Any help in terms of raw commands to use is welcome.
Dorian
On Tue, Jan 31, 2017 at 4:52 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You can smooth it. This would give you a gaussian kernel instead of the box kernel that you describe. Set the fwhm to the radius you want (mris_fwhm with --smoothonly option)
On 01/31/2017 04:48 PM, Dorian P. wrote:
Hi Freesurfers,
Thank you for the help you provide through this list.
Is there a way to get, for each vertex, the identify (or thickness values) of the surrounding vertices in a 10mm radius? The command mris_convert has the '-v' option, but that produces only 5-6 vertices and there is no option to query a particular radius.
I imagine this can be done manually outside Freesurfer by first identifying the neighbors for each vertex based on the coordinates, then getting the respective thickness value, but I wanted to check whether there is any easier way or any advice on how to proceed.
Dorian
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