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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
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