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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
<bfis...@mgh.harvard.edu<mailto:bfis...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto: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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