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Thanks Bruce and Yujing! Bruce — the fslorient changes the ras2vox (i.e., the
(1,1) entry of the ras to voxel transform is multiplied by -1, when
fslorient-ing to LAS orientation).
Best,
Panos
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD
<bfis...@mgh.harvard.edu>
Date: Tuesday, January 23, 2024 at 12:26 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MRIread and RAS orientation
Does fslorient resample or just change the ras2vox?
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Fotiadis, Panagiotis
Sent: Tuesday, January 23, 2024 12:11 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MRIread and RAS orientation
External Email - Use Caution
Thanks, Bruce! Just to reiterate my previous message below, would you happen to
know why the MRI.vol matrices of both files come out looking identical?
-----------
… 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?
-----------
Thank you all again!
Best,
Panos
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce R.,PHD
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>>
Date: Tuesday, January 23, 2024 at 11:06 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] MRIread and RAS orientation
I agree with Eugenio – it doesn’t do any resampling. Just reads in the data as
is
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Huang, Yujing
Sent: Tuesday, January 23, 2024 8:49 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto: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<mailto: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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