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I think it should work ok. If you want to run it in native space, add -conform-dc (but this should be done for everyone in your study). Conforming like this was started in FS 25 years ago and for reprodicibility purposes, we've kept it there by default (but added the -conform-dc).
On 6/21/2023 5:42 PM, Ruifeng Dong wrote:
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Dear all,
We acquired the images (sagittal, 176*256*256) with obliqueness, because we tried to match the prescription with the subject's head positioning. Then, the obliqueness is shown in the header of the image.
We used this image in recon-all. After mri_convert --conform, Freesurfer reoriented the image to RSP and then changed to 256*256*256 FOV. As a result, in orig.mgz, the image is tilted. Wouldn't this make it harder for Freesurfer to register with the template?
Why does Freesurfer do this? Does it only expect input images with no obliqueness, i.e. anatomical coordinates and physical coordinates are always aligned?
Thank you!
Best, Ruifeng
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