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

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

Thanks and I presume that surfaceRAS coordinates are intrinsically in mm?

Jerry

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@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-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

---

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 greve@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.htmlhttp://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.

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-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