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
<dgr...@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
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