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Hi Bruce,
Yes I read in the patch the way that you're suggesting and I can access the vino for the flat map. But how do i know the vertex number of each vertex in the pial surface? Are they in order ?
Also, what coordinate system is the pial surface in when its read into FreeSurfer? Is it RAS or surface RAS?
Kind Regards, Ornaith
On Wed, 7 Apr 2021 at 20:02, Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
How do you read it in? If you are using the read_patch.m that we distribute it should be stored in patch.vno if you do:
patch = read_patch(path_file_name)
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Ornaith O Reilly *Sent:* Wednesday, April 7, 2021 2:29 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Cortical surface analysis
External Email - Use Caution *Hi Bruce,
Thanks so much for your quick reply, I really appreciate your help on this.
I don't understand how to recover the vertex index.
In Freeview I can see the vertex index number. When I load in the data to MATLAB as discussed - the only thing that I have access to are the coordinates of the vertices - not the vertex index. How can I recover the vertex indices as well?
Thanks again.
Kind Regards,
Ornaith
On Tue, 6 Apr 2021 at 19:31, Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Hi Ornaith
The mapping uses the vertex index. That is, the vertex index is stored in the flatmap, so you should always be able to recover it, then look up the location of that vertex on any other surface (of the same hemisphere/subject)
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Ornaith O Reilly *Sent:* Tuesday, April 6, 2021 2:19 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Cortical surface analysis
External Email - Use Caution *Hello FreeSurfer developers,
Thanks a lot for your help. I have initialised the pialxyz the way you suggested and made the flatmap in MatLab using the read_patch function (screenshots attached). I still don't understand how to convert between the two. For example how to see what point (x,y,z) on the pial surface corresponds to what (x,y) point on the flatmap.
Thanks a lot for your help.
Kind Regards,
Ornaith
On Tue, 16 Mar 2021 at 15:58, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
On 3/8/2021 11:38 AM, Ornaith O Reilly wrote:
External Email - Use Caution *Hello Freesurfer developers,
I am new to Freesurfer and I'm hoping that someone can help me.
My goal is to be able to visualise electrodes contacts that are on lying on the cortical surface on a flat map and a spherical map.
I've run recon-all and created the flatmap.
I'm using Matlab to achieve this and I've loaded the information with the lines
lhsphere = fs_read_surf( '/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.sphere');
lhflatpatch=fs_read_patch( '/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.full.flat.patch.3D' );
- I want to be able to access the coordinates and show the electrons on
the flat map/ sphere and I was wondering how to do this? I understand that the vertex ID number is what relates the coordinates in the original image to these surfaces. I am wondering how to access the vertex ID numbers ? At the moment I think that I only have access to the vertex coordinates and the vertex faces.
The easiest way to do this is probably to map the white or pial xyz into an mgz file using mri_surf2surf, eg mri_surf2surf --hemi lh --sval-xyz white --tval lh.white.xyz.mgz --s yoursubject You can then get the xyz of a given vertex by reading whitexyz = MRIread('lh.white.xyz.mgz');
- Additionally, I was wondering if there is a way to display the surface
images through Matlab? What would be the best way to show the surface with the electrons overlaid on it?
I know there are ways, but I don't know their details
The version of Freesurfer and the platform that I'm using is outlined below:
FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
Platform: macOS High Sierra 10.13.6 (17G7024)
I really appreciate any help with this as I'm really stuck.
Thanks in advance for any help.
Kind Regards,
Ornaith O'Reilly
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