Hi Ali

If you use read_patch.m I believe it returns a structure that has the original vertex index in it. It’s been a *long* time since I looked at that code, but it looks like we actually store it twice for some reason:

for i=1:patch.npts

    ind = fread(fid, 1, 'int', 0, 'b') ;

    if (ind < 0)

       ind = -ind - 1 ;

    else

       ind = ind - 1 ;

    end

    patch.ind(i) = ind ;

    patch.x(i) = fread(fid, 1, 'float', 0, 'b') ;

    patch.y(i) = fread(fid, 1, 'float', 0, 'b') ;

    patch.z(i) = fread(fid, 1, 'float', 0, 'b') ;

    patch.vno(i) = ind ;

end

so patch.vno should be the original vertex number, which you can use to index into any of the other surfaces (for that subject/hemi)

cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Alison McDonnell
Sent: Wednesday, March 30, 2022 11:45 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FREESURFER Maintaining vertex Id during transformations

        External Email - Use Caution        

Hi Bruce, 

If I have the coordinate on the flat map how do I get the corresponding vertex ID? And then from that same ID get the 3D coordinates?

Ali 

On Wed, 30 Mar 2022 at 16:09, Fischl, Bruce <BFISCHL@mgh.harvard.edu> wrote:

Hi Ali

We keep track of the vertex index of the flat maps, so you should just be able to use it to look up the coordinate of whatever other (white, pial) surface you want, then see what volumetric coordinates it is at

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Alison McDonnell
Sent: Wednesday, March 30, 2022 11:04 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] FREESURFER Maintaining vertex Id during transformations

        External Email - Use Caution        

Hi all,

I have been able to create my flat map in freesurfer and then do calculations using it to find a point. I then want to map that point back into the 3D space maintaining the coordinates. I was wondering if anyone had done something similar before and had any ideas. I am using MATLAB for the calculations and transformations. 

Ali 

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