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Dear FreeSurer Wizards,
I'm trying to run the recon-all command on one of my template brains such that the resulting Norig and Torig are identical. I understand that fs always conforms the MRI to 256^3 before segmentation. I wonder if there is any way that I can resample the original MRI to achieve the same Norig and Torig?
More specifically, currently the Torig (vox to tkrRAS) is [,1] [,2] [,3] [,4] [1,] -1 0 0 128 [2,] 0 0 1 -128 [3,] 0 -1 0 128 [4,] 0 0 0 1
If I resample the input image such that Norig (vox to scanRAS) equals this matrix, can I expect that "conform" does not change the orientation?
Alternatively, is there any method I can use to "predict" or reproduce the Torig from the original MRI outside of FreeSurfer?
Thanks, - Dipterix
If you want to keep the original orientation, you can specify --conform-dc. Would that fix your problem?
On 12/21/2023 9:30 AM, Dipterix Wang wrote:
External Email - Use Caution
Dear FreeSurer Wizards,
I'm trying to run the recon-all command on one of my template brains such that the resulting Norig and Torig are identical. I understand that fs always conforms the MRI to 256^3 before segmentation. I wonder if there is any way that I can resample the original MRI to achieve the same Norig and Torig?
More specifically, currently the Torig (vox to tkrRAS) is [,1] [,2] [,3] [,4] [1,] -1 0 0 128 [2,] 0 0 1 -128 [3,] 0 -1 0 128 [4,] 0 0 0 1
If I resample the input image such that Norig (vox to scanRAS) equals this matrix, can I expect that "conform" does not change the orientation?
Alternatively, is there any method I can use to "predict" or reproduce the Torig from the original MRI outside of FreeSurfer?
Thanks,
- Dipterix
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
I tried `--conform-dc` and the flag was not recognized. `-conform-dc` didn't give me error. However, vox2ras-tkr still didn't include the cosine information.
This is the Torig:
mri_info --vox2ras-tkr T1.mgz
-1.00000 0.00000 0.00000 128.00000
0.00000 0.00000 1.00000 -128.00000
0.00000 -1.00000 0.00000 128.00000
0.00000 0.00000 0.00000 1.00000
While Norig is
mri_info --vox2ras T1.mgz
-0.99989 0.00604 0.01331 124.66034
0.01408 0.15990 0.98703 -164.17455
-0.00383 -0.98711 0.15997 108.14072
0.00000 0.00000 0.00000 1.00000
I wonder what steps I could take to make sure the Torig = Norig. Here Norig is acpc realigned.
Best, - D
On Mon, Jan 1, 2024 at 4:27 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
If you want to keep the original orientation, you can specify --conform-dc. Would that fix your problem?
On 12/21/2023 9:30 AM, Dipterix Wang wrote:
External Email - Use CautionDear FreeSurer Wizards,
I'm trying to run the recon-all command on one of my template brains such that the resulting Norig and Torig are identical. I understand that fs always conforms the MRI to 256^3 before segmentation. I wonder if there is any way that I can resample the original MRI to achieve the same Norig and Torig?
More specifically, currently the Torig (vox to tkrRAS) is [,1] [,2] [,3] [,4] [1,] -1 0 0 128 [2,] 0 0 1 -128 [3,] 0 -1 0 128 [4,] 0 0 0 1
If I resample the input image such that Norig (vox to scanRAS) equals this matrix, can I expect that "conform" does not change the orientation?
Alternatively, is there any method I can use to "predict" or reproduce the Torig from the original MRI outside of FreeSurfer?
Thanks,
- Dipterix
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1tO0Wjb5ekjKkkZoaygATt42ODvCqJv-XfhqZbSqJhF3k_D... 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://secure-web.cisco.com/1spdzsTy5nH-y6bhSLJq2Wcin8crxFnBzpkWIRA_IIjHmYP... < https://secure-web.cisco.com/1spdzsTy5nH-y6bhSLJq2Wcin8crxFnBzpkWIRA_IIjHmYP... .
The TkR vox2ras will never have direction cosine info. The -conform-dc will keep the original DC in the "conformed" volume (eg, orig.mgz vs rawavg.mgz)
On 1/11/2024 3:22 PM, Dipterix Wang wrote:
External Email - Use Caution
I tried `--conform-dc` and the flag was not recognized. `-conform-dc` didn't give me error. However, vox2ras-tkr still didn't include the cosine information.
This is the Torig:
mri_info --vox2ras-tkr T1.mgz
-1.00000 0.00000 0.00000 128.00000
0.00000 0.00000 1.00000 -128.00000
0.00000 -1.00000 0.00000 128.00000
0.00000 0.00000 0.00000 1.00000
While Norig is
mri_info --vox2ras T1.mgz
-0.99989 0.00604 0.01331 124.66034
0.01408 0.15990 0.98703 -164.17455
-0.00383 -0.98711 0.15997 108.14072
0.00000 0.00000 0.00000 1.00000
I wonder what steps I could take to make sure the Torig = Norig. Here Norig is acpc realigned.
Best,
- D
On Mon, Jan 1, 2024 at 4:27 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
If you want to keep the original orientation, you can specify --conform-dc. Would that fix your problem? On 12/21/2023 9:30 AM, Dipterix Wang wrote:External Email - Use Caution Dear FreeSurer Wizards, I'm trying to run the recon-all command on one of my template brains such that the resulting Norig and Torig are identical. I understand that fs always conforms the MRI to 256^3 before segmentation. I wonder if there is any way that I can resample the original MRI to achieve the same Norig and Torig? More specifically, currently the Torig (vox to tkrRAS) is [,1] [,2] [,3] [,4] [1,] -1 0 0 128 [2,] 0 0 1 -128 [3,] 0 -1 0 128 [4,] 0 0 0 1 If I resample the input image such that Norig (vox to scanRAS) equals this matrix, can I expect that "conform" does not change the orientation? Alternatively, is there any method I can use to "predict" or reproduce the Torig from the original MRI outside of FreeSurfer? Thanks, - Dipterix _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1pypFkk7agGEz-slZaaob7MhUratnBnS-4EywhwYEIGmLHK84Q8p2d3iC1ZcQdn7qb1Aaj9OatRlhnm46AiXky63YJkhEaIh_1by5p5iyTRL-p-BsjRp6HJq-pmo5pJ0KSLouOYfZ0t6tgO5ZBXV0FgB8_YjVz1jtd_9B39Bs-qxX_ULdLFHHpKecncdQLVGm0cy2igcUIL8A3l2xSqGBFvMixpjmPsa_9W-xKwrZPBbNGmqsSYRw-RzZlmYA3e9P9DcdcLRM75TwhTMogOiLAUUcuTZknWKLWBzTzPKliKede_dhlVthpTGlVgAPK1Bg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1pypFkk7agGEz-slZaaob7MhUratnBnS-4EywhwYEIGmLHK84Q8p2d3iC1ZcQdn7qb1Aaj9OatRlhnm46AiXky63YJkhEaIh_1by5p5iyTRL-p-BsjRp6HJq-pmo5pJ0KSLouOYfZ0t6tgO5ZBXV0FgB8_YjVz1jtd_9B39Bs-qxX_ULdLFHHpKecncdQLVGm0cy2igcUIL8A3l2xSqGBFvMixpjmPsa_9W-xKwrZPBbNGmqsSYRw-RzZlmYA3e9P9DcdcLRM75TwhTMogOiLAUUcuTZknWKLWBzTzPKliKede_dhlVthpTGlVgAPK1Bg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> 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://secure-web.cisco.com/1J3DY6pxfhF5LRnayhks49YYErrMcEepaiQSZmr7TPmrq9-2ZAhAVhEWaB6AFYX6ftGWnIK2_j7xLOVPZ8nXJAWCg6uzArz0WZ_8QhIV6gX2byWulAr4H8HR-tnkyiCMa4ffKWR3E_7YqQHrDsAiWXWltwi5X8BItSeN_AqCPO08VY9k73d6MZXX4Rsn0vXJCOTXAK8chZQltOYJk50Dt0OyNy9IdwgxD3ABAIrkY5JGttVEw-ENUGw_jMZCYTaSw9lBwR7S6B1hO7DOakGcr4Bi10ntSlXYjGG07uI_B4OVyYJXIEX__C9QTRK3M_wn8/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1J3DY6pxfhF5LRnayhks49YYErrMcEepaiQSZmr7TPmrq9-2ZAhAVhEWaB6AFYX6ftGWnIK2_j7xLOVPZ8nXJAWCg6uzArz0WZ_8QhIV6gX2byWulAr4H8HR-tnkyiCMa4ffKWR3E_7YqQHrDsAiWXWltwi5X8BItSeN_AqCPO08VY9k73d6MZXX4Rsn0vXJCOTXAK8chZQltOYJk50Dt0OyNy9IdwgxD3ABAIrkY5JGttVEw-ENUGw_jMZCYTaSw9lBwR7S6B1hO7DOakGcr4Bi10ntSlXYjGG07uI_B4OVyYJXIEX__C9QTRK3M_wn8/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> .
freesurfer@nmr.mgh.harvard.edu
-
Dipterix Wang -
Douglas N. Greve