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>
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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