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:

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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

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