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:
External Email - Use Caution
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If
the e-mail was sent to you in error but does not contain patient information,
please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
