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
> >
> >
> >
>
>