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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
<fis...@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-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
> <fis...@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
> >
> >
> >
>
>
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