How did you generate the nii file from the mesh?
On 6/29/2020 12:21 PM, Franziska Klein wrote:
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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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