Hi Jerry
we have code that does this internally, but nothing that is easy to use from the command line. You could do what you suggest using the lh.sphere to compute distance. That will avoid the problem of crossing the banks of a sulcus
cheers Bruce On Wed, 10 May 2017, Jerry Jeyachandra wrote:
Hi Bruce,
To clarify, if I were to use:
mris_convert lh.pial lh.pial.asc
That would give me surfaceRAS coordinates for the vertices for the lh.pial surface which is consistent in order for the vertex normals in lh.pial.normals.asc? I find this easier to work with than mri_surf2surf since my filepaths within a subject directory are non-standard for freesurfer.
If I may ask another question, is there a method available for identifying all the vertices within x mm radius on the surface expanding from a specified point? I am thinking of simply using the euclidean distance as a "good enough" approximation given the resolution but am not sure about how that would convert to mm measurements to specify the x mm radius.
My end goal is to compute an average surface normal for a region specified by a given radius for each subject.
Apologies for being naive, I'm very new to using freesurfer
Thanks,
Jerry
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: May 9, 2017 3:40:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Obtaining surface normal vector from plial surfaceRAS coordinate when you specify -n it write out surface normals instead of surface locations. Or you can use Doug's method
cheers Bruce On Tue, 9 May 2017, Jerry Jeyachandra wrote:
Hi Bruce,
Thanks for the response. I've run the operation and have examined the output. From my understanding the file contains both a vertex list (XYZ)
and
a face list containing (V1,V2,V3...). Is the XYZ of the vertex list the actual surfaceRAS coordinates of the surface as viewed on FreeViewer? If
so
I can compute face normals simply by matching up the 3 vertices encapsulating the given surface coordinate and computing the face normal vector, correct?
Thanks again
Jerry
_
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: May 8, 2017 4:40:17 PM To: Freesurfer support list Subject: Re: [Freesurfer] Obtaining surface normal vector from plial surfaceRAS coordinate Hi Jerry
mris_convert -n lh.pial lh.pial.normals.asc
should create a list of surface normals in ascii format
cheers Bruce On Mon, 8 May 2017, Jerry Jeyachandra wrote:
Hi list,
I’d like to extract the surface normal at a location specified in
surfaceRAS
coordinates after performing segmentation. I know there are methods to extract all vertices and faces then compute face normals from there, but
I’m
not familiar with methods to relate these to specified coordinates.
Thanks
Jerry Jeyachandra