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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