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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Pawel
March 22, 2022 10:59AM
Hi Daniel,

thank you, adding:
-master_epi BASE
to align_epi_anat.py options solved the issue,

Just to see how it works I tried to go through 3dWarp too, but with no -gridset applied it cropped the T2 in the same way as in my original post.

However, providing the T1 as the gridset produced a virtually identical result to align_epi_anat.py with -master_epi BASE (minute differences I guess due to different interpolation method). So I could go either way though -master_epi BASE is obviously more convenient, no additional step as opposed to two additional steps (3dWarp precede by onverting the transform from 12x1 to 3x4 format).

Thanks again, and I apologize that - as I just noticed - I did not include my full align_epi_anat.py call in the first post. I intended to!
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align_epi_anat cropping Attachments

Pawel March 18, 2022 02:07PM

Re: align_epi_anat cropping

Daniel Glen March 21, 2022 06:58PM

Re: align_epi_anat cropping

Pawel March 22, 2022 10:59AM

Re: align_epi_anat cropping

Daniel Glen March 22, 2022 11:03PM