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Hi Bruce,
Thanks a lot for this. What is the difference between RAS and surface RAS?
Do I need to convert the surface RAS into RAS to be dealing in the volume
space?
Kind Regards,
Ornaith
On Tue, 27 Apr 2021 at 15:44, Fischl, Bruce <bfis...@mgh.harvard.edu> wrote:
> All the surface vertices are just listed in order. The patch keep track of
> which vertex it corresponds to (so you can just use pial_surface[patch.vno]
> or something).
>
>
>
> The coordinates are documented on our website and are “surface ras”.
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Ornaith O Reilly
> *Sent:* Tuesday, April 27, 2021 8:02 AM
> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] Cortical surface analysis
>
>
>
> * External Email - Use Caution *
>
> 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 <bfis...@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-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@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 <bfis...@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-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>
> 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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