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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
<dgr...@mgh.harvard.edu<mailto:dgr...@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');
1. 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');
2. 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:
1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
2) 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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