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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

********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

I agree with Eugenio - it doesn't do any resampling. Just reads in the data as is

Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fotiadis, Panagiotis Sent: Tuesday, January 23, 2024 1:54 AM To: freesurfer@nmr.mgh.harvard.edumailto: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

********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

Does fslorient resample the image to have the data on disk reoriented? If not, as Bruce and Eugenio commented, it is reading the same data with same orientation.

I think you can use ‘mri_diff --notallow-geo f1 f2’ to check if f1 and f2 have the same data orientation on disk.

You can use ‘mri_vol2vol --mov <movimage> --targ <targimage> --regheader --o <outimage> --interp nearest’ to reorient the data.

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 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Date: Tuesday, January 23, 2024 at 11:06 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fotiadis, Panagiotis Sent: Tuesday, January 23, 2024 1:54 AM To: freesurfer@nmr.mgh.harvard.edumailto: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

********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Date: Tuesday, January 23, 2024 at 11:06 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fotiadis, Panagiotis Sent: Tuesday, January 23, 2024 1:54 AM To: freesurfer@nmr.mgh.harvard.edumailto: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

********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues