date:20240123

Re: [Freesurfer] MRIread and RAS orientation

2024-01-23 Thread Fotiadis, Panagiotis

External Email - Use Caution

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 
 on behalf of Fischl, Bruce R.,PHD 

Date: Tuesday, January 23, 2024 at 12:26 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] MRIread and RAS orientation
Does fslorient resample or just change the ras2vox?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fotiadis, Panagiotis
Sent: Tuesday, January 23, 2024 12:11 PM
To: Freesurfer support list 
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  in file1.vol had the exact same value as voxel 
in location  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>>
 on behalf of Fischl, Bruce R.,PHD 
mailto:bfis...@mgh.harvard.edu>>
Date: Tuesday, January 23, 2024 at 11:06 AM
To: Freesurfer support list 
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>>
 On Behalf Of Huang, Yujing
Sent: Tuesday, January 23, 2024 8:49 AM
To: Freesurfer support list 
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>>
 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

**
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used for urgent or sensitive issues
**
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used for urgent or sensitive issues 
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Re: [Freesurfer] MRIread and RAS orientation

2024-01-23 Thread Fischl, Bruce R.,PHD

Does fslorient resample or just change the ras2vox?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fotiadis, Panagiotis
Sent: Tuesday, January 23, 2024 12:11 PM
To: Freesurfer support list 
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  in file1.vol had the exact same value as voxel 
in location  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>>
 on behalf of Fischl, Bruce R.,PHD 
mailto:bfis...@mgh.harvard.edu>>
Date: Tuesday, January 23, 2024 at 11:06 AM
To: Freesurfer support list 
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>>
 On Behalf Of Huang, Yujing
Sent: Tuesday, January 23, 2024 8:49 AM
To: Freesurfer support list 
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>>
 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

**
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used for urgent or sensitive issues
___
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Re: [Freesurfer] MRIread and RAS orientation

2024-01-23 Thread Huang, Yujing

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  --targ  --regheader --o 
 --interp nearest’ to reorient the data.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fotiadis, Panagiotis
Sent: Tuesday, January 23, 2024 12:11 PM
To: Freesurfer support list 
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  in file1.vol had the exact same value as voxel 
in location  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>>
 on behalf of Fischl, Bruce R.,PHD 
mailto:bfis...@mgh.harvard.edu>>
Date: Tuesday, January 23, 2024 at 11:06 AM
To: Freesurfer support list 
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>>
 On Behalf Of Huang, Yujing
Sent: Tuesday, January 23, 2024 8:49 AM
To: Freesurfer support list 
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>>
 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

**
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used for urgent or sensitive issues
___
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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continue to communicate over unencrypted e-mail.

Re: [Freesurfer] MRIread and RAS orientation

2024-01-23 Thread Fotiadis, Panagiotis

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  in file1.vol had the exact same value as voxel 
in location  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 
 on behalf of Fischl, Bruce R.,PHD 

Date: Tuesday, January 23, 2024 at 11:06 AM
To: Freesurfer support list 
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 
 On Behalf Of Huang, Yujing
Sent: Tuesday, January 23, 2024 8:49 AM
To: Freesurfer support list 
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>>
 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
**
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used for urgent or sensitive issues 
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] MRIread and RAS orientation

2024-01-23 Thread Fischl, Bruce R.,PHD

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 
 On Behalf Of Huang, Yujing
Sent: Tuesday, January 23, 2024 8:49 AM
To: Freesurfer support list 
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>>
 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
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
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continue to communicate over unencrypted e-mail.

Re: [Freesurfer] MRIread and RAS orientation

2024-01-23 Thread Fotiadis, Panagiotis

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  in 
file1.vol had the exact same value as voxel in location  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 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Date: Tuesday, January 23, 2024 at 9:14 AM
To: Freesurfer support list 
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/1AMDDl8zoTx97KmWakLJs6Eb2300KbZd5XLRRIg8thUrLDGjU9dvlwys4jeGWIZTxIAUTnyzpDtbVLWaNODwHXUjmOtoQkKntKWL7e7jSVR5_2H_htfNkhmM2PHcl5C80J9wFgwvHBX1VBcfrEpVuzZQ4yFXH5-0nkBurBI4uhVT2YspEod5yfAPBiODTQpPdopg-2yCq9qh444-D6-sUguKrij6_yxGkeWpLJ6nbYIUlh1kTTYxUxudSQf5Fh17nO8xfca5RP58SQEiNzxZGlhXSdtd61CYLWI2mII81Sm4mZFOQCAd3lCQLGachEhze/http%3A%2F%2Fwww.jeiglesias.com

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Date: Tuesday, January 23, 2024 at 08:49
To: Freesurfer support list 
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 
 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 
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
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Re: [Freesurfer] MRIread and RAS orientation

2024-01-23 Thread Iglesias Gonzalez, Juan E.

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 
 on behalf of Huang, Yujing 

Date: Tuesday, January 23, 2024 at 08:49
To: Freesurfer support list 
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 
 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
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Re: [Freesurfer] File extension .area failures

2024-01-23 Thread Huang, Yujing

Not sure what kind of server you are running. Maybe your IT can help with the 
file extension issue.

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of James Bartolotti
Sent: Monday, January 22, 2024 6:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] File extension .area failures

External Email - Use Caution
The MR data on network drives at our institute were recently migrated to a new 
server. After the migration, recon-all in freesurfer fails to complete. The 
issue is that freesurfer generates files with the extension ".area", including 
lh.area and rh.area, but the .area extension is forbidden on the server and the 
files will not be created.

Has anyone ever had issues with an .area extension? Are there any possible 
workarounds to change the .area extension used by freesurfer?

James Bartolotti, Ph.D. (he/him/his)

Senior Scientist

Structure and Function Unit, Hoglund Biomedical Imaging Center

University of Kansas Medical Center

jbartolot...@kumc.edu
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Re: [Freesurfer] MRIread and RAS orientation

2024-01-23 Thread Huang, Yujing

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 
 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] MRIread and RAS orientation

Re: [Freesurfer] MRIread and RAS orientation

Re: [Freesurfer] MRIread and RAS orientation

Re: [Freesurfer] MRIread and RAS orientation

Re: [Freesurfer] MRIread and RAS orientation

Re: [Freesurfer] MRIread and RAS orientation

Re: [Freesurfer] MRIread and RAS orientation

Re: [Freesurfer] File extension .area failures

Re: [Freesurfer] MRIread and RAS orientation

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