yes
On 05/10/2017 12:50 PM, Jerry Jeyachandra wrote: > > Thanks and I presume that surfaceRAS coordinates are intrinsically in mm? > > Jerry > > ------------------------------------------------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > <gr...@nmr.mgh.harvard.edu> > *Sent:* May 10, 2017 12:42:29 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Obtaining surface normal vector from plial > surfaceRAS coordinate > We don't have a way to compute the exact distance from one vertex to > another along the surface (working on it!). If the distances are small, > then euclidian might work ok. > > > On 05/10/2017 12:35 PM, 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 > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
