Re: [Freesurfer] MRIread and RAS orientation
The vol structure will reflect how the volume is stored on disk. If you have two files that have the same structure (ie, order of rows, cols, slices) then they will have the same vol in matlab regardless of the header orientation. On 1/23/2024 11:00 AM, Fotiadis, Panagiotis wrote: 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://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 ** 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . 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
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> 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> 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> 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 ** 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 ___ 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 continue to communicate over unencrypted e-mail.
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> 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> 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> 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 ** 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 continue to communicate over unencrypted e-mail.
Re: [Freesurfer] MRIread and RAS orientation
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> 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> 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> 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 ** 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 continue to communicate over unencrypted e-mail.
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 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> 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 ** 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 continue to communicate over unencrypted e-mail.
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> 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 ** 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 continue to communicate over unencrypted e-mail.
Re: [Freesurfer] MRIread and RAS orientation
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 continue to communicate over unencrypted e-mail.
Re: [Freesurfer] MRIread and RAS orientation
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 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
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 receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[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 receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
