Not really. If you pass it an input that is already ACPC, you can add -conform-dc to keep the orientation.
On 10/14/2021 9:44 AM, Zhengchen Cai wrote:
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Hello FreeSurfer Developers,
I wonder if we have a function that could automatically align T1w to ACPC before running recon-all? Or if we have an option in recon-all that could do this ACPC alignment automatically? I noticed there are such ways after running freesurfer by applying the transformation matrix, but I guess it will be less convenient than pre-alignment since we don't bother to transform all the output. Especially if we use freesurfer with other tools like fMRIPrep, all functional images will also be registered to ACPC aligned T1w. I ask this since sometimes the T1w is tilted and not desirable for visualization purposes. Thanks a lot.
Best regards, Zhengchen
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