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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