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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rick reynolds
September 08, 2015 12:54PM
Hi,

It might be worth pointing out that afni_proc.py will
actually run align_epi_anat.py for you if the 'align'
processing block is included. See example 6 and later
in the -help output:

afni_proc.py -help

Getting to your questions...

The base volume should be the same as the base volume
used in EPI alignment (3dvolreg). Otherwise, 3dvolreg
might undo the gain from align_epi_anat.py.

This has little to do with slice timing, which aligns
to a time within a TR, or maybe to a slice time within
the times from a volume. There is no volume chosen for
slice timing correction, but rather a slice.

- rick
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Subject Author Posted

Anat/EPI alignment considerations

hbfwjC September 07, 2015 05:07AM

Re: Anat/EPI alignment considerations

rick reynolds September 08, 2015 12:54PM