Re: [Freesurfer] MRIread and RAS orientation

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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@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://secure-web.cisco.com/1AMDDl8zoTx97KmWakLJs6Eb2300KbZd5XLRRIg8thUrLDGj...

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

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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