AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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herrlich10
October 14, 2018 11:18AM
Hi afni experts,

I have a pair of T1 and EPI which I manually coregistered (for some reason) in FreeSurfer, using the following command:
tkregister2 --s subj_id --mov epi.nii --surf orig --reg register.dat --regheader

Now with the affine transform matrix at hand (in the register.dat file), I would like to apply it to the T1 volume in AFNI, using 3dAllineate.

However, due to the incompatible coordinates conventions between FS and AFNI (e.g., RAS vs RAI) I guess, or difference in volume orientations, or some other reasons, the matrix in register.dat doesn't work in its raw form.

So how to apply affine transform matrix generate by FreeSurfer using 3dAllineate?

Thank you!
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Apply affine transform generated by freesurfer using afni

herrlich10 October 14, 2018 11:18AM