I’m pretty sure that the Matlab code does not reorient.

Cheers,

Eugenio

--

Juan Eugenio Iglesias

http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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

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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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