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

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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