External Email - Use Caution
I know, a lot of steps.
1-based vs. 0-based, that is basically what I mean and what I think is the
problem, but I need to be sure. When I load in the *.nii file generated from
the mesh and display it in SPM, then the origin shown in the SPM Gui is the
last column in vox2ras1. Oversimplified, when I want to compare a voxel from
SPM with a voxel from freesurfer, I need to shift the coordinates of that voxel
from freesurfer by +1, right? (or substract one from the SPM one).
Kind regards,
Franziska
________________________________
Von: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Douglas N. Greve
<dgr...@mgh.harvard.edu>
Gesendet: Montag, 29. Juni 2020 16:44:34
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Question regarding MRIread
There's a lot of stuff going on there, so it's hard to say withhout more
detail. But it sounds like you might not be taking into account that the voxel
coords in matlab are 1-based.
On 6/26/2020 12:04 PM, Franziska Klein wrote:
External Email - Use Caution
Hello,
I am using the isosurface() function in order to create a mesh based on the
T1.mgz and on the ribbon.mgz. I need those meshes for the coregistration of
some channels.
After coregistration I do project the channels onto the cortex and extract the
corresponding voxel coordinates. Until here, everything works fine.
Next, I am using MRIwrite in order to save the T1.mgz as *.nii.mgz which I am
using to generate a deformation field with SPM12 to transform the voxel
coordinates to normalized MNI coordinates. However, when I put the voxel
coordinates (not normalized yet) into SPM12 while displaying my generated *.nii
image it happens that the coordinates on the right hemisphere (MNI space) are
slightly outside of the cortex which is of course not the case on my cortex
mesh after projection.
Now I am wondering whether there is a mismatch between the mesh and the *.nii
image (one voxel maybe)? And whether that is introduced by MRIwrite? If so, do
I have to shift all points of the meshes by +1 in order to get correct results
the way I want to? If not, any ideas on where that mismatch could come from?
Thank you and kind regards,
Franziska
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