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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gchahine
September 08, 2017 07:18PM
Thank you pt and RWCox.
I "deobliqued" my EPI and then used @Align_Centers to center the EPI and the skull stripped anatomical at the center of mass before running afni_proc.py and this seems to have solved the issue. I don't think I need -giant_move or use another cost function just yet.

Are there any concerns for aligning the EPI and the anatomical before running the other preprocessing steps? I think this was suggested somewhere on the forum prior.

I am also encountering a warning message from 3dTStat : "Input dataset is not 3D+time; assuming TR=1.0". Should I be concerned? The registration and the alignment seem pretty good now.

Regards,
George
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Subject Author Posted

Manual realignment

gchahine September 07, 2017 10:46PM

Re: Manual realignment

ptaylor September 08, 2017 08:22AM

Re: Manual realignment

gchahine September 08, 2017 09:08AM

Re: Manual realignment

ptaylor September 08, 2017 09:47AM

Re: Manual realignment

gchahine September 08, 2017 07:18PM

Re: Manual realignment

gchahine September 09, 2017 07:22AM

Re: Manual realignment

RWCox September 08, 2017 11:22AM

Re: Manual realignment

rosaann September 14, 2017 04:00AM

Re: Manual realignment

RWCox September 14, 2017 06:25AM