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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Matthew Hoptman
January 23, 2023 02:08PM
Hi all,
I recently read your article (Glen et al., 2020). I have a question based on it/check_flip.

I have images that were acquired in RPI orientation (verified with a vitamin E capsule. When I ran align_epi_anat.py, I get the outcome NO_FLIP (using the raw images as input). So far, so good.

However, previously, I had reoriented the mprage and epi images to RAI (as I know that is the afni default) and then deobliqued them. I reoriented them using 3drefit -orient RAI. When I use THESE Images as the input to align_epi_anat.py, the outcome is DO_FLIP.

Could you please explain why this might happen?
Thanks,
Matt
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Subject Author Posted

-check_flip

Matthew Hoptman January 23, 2023 02:08PM

Re: -check_flip

ptaylor January 23, 2023 04:29PM

Re: -check_flip

Matthew Hoptman January 23, 2023 05:04PM

Re: -check_flip

Matthew Hoptman January 23, 2023 06:34PM

Re: -check_flip

Daniel Glen January 23, 2023 05:04PM

Re: -check_flip

Matthew Hoptman January 23, 2023 06:54PM