The vol structure will reflect how the volume is stored on disk. If you
have two files that have the same structure (ie, order of rows, cols,
slices) then they will have the same vol in matlab regardless of the
header orientation.
On 1/23/2024 11:00 AM, Fotiadis, Panagiotis wrote:
External Email - Use Caution
Thank you both! I am asking because I took a nifti file that was in
RAS orientation (file1), flipped it into LAS (using /fslorient
-swaporient file2/), and then opened both files in MATLAB with
MRIread. The resulting .vol matrices for both files were, however,
identical (i.e., voxel at location <x,y,z> in file1.vol had the exact
same value as voxel in location <x,y,z> in file2.vol). Would you
happen to know if the indexing of the vol structure is expected to
come out the same with MRIread, regardless of the orientation?
Thanks,
Panos
*From: *freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias
Gonzalez, Juan E. <jiglesiasgonza...@mgh.harvard.edu>
*Date: *Tuesday, January 23, 2024 at 9:14 AM
*To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] MRIread and RAS orientation
*External Email - Use Caution *
I’m pretty sure that the Matlab code does not reorient.
Cheers,
Eugenio
--
Juan Eugenio Iglesias
http://www.jeiglesias.com
*From: *freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu>
*Date: *Tuesday, January 23, 2024 at 08:49
*To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] MRIread and RAS orientation
I’m not sure about the MATLAB codes. When the C codes read in images,
no automatically transformation is done.
I think you can verify it by checking several [c, r, s] locations of
both images loaded with MRIread(). I think c and r are reversed in
MATLAB. And the index starts from 1.
Best,
Yujing
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Fotiadis,
Panagiotis
*Sent:* Tuesday, January 23, 2024 1:54 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] MRIread and RAS orientation
* External Email - Use Caution *
Hello,
I have two nifti files that are both in the same MNI space, the former
of which is saved in LAS orientation while the other in RAS
orientation (as showcased by the “Orientation” field of mri_info). I
just wanted to verify: When loading both on MATLAB using MRIread, both
of their volumes are automatically loaded (or transformed in the case
of the first file) in the same RAS orientation, right (using the
vox2ras transformation)?
Thanks in advance!
Best,
Panos
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