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
February 23, 2009 06:17PM
Hi Steve,

That is correct, but it is on "the list".

The downside of using 3dWarp on the EPI data is the extra resample
step. The most simple method for dealing with it is to use 3dWarp
to transform the anat to the oblique EPI via -card2oblique. After
that all of your data is still oblique, but it is oblique the same
way. So it would be okay to use '3drefit -deoblique' on it (just
to shut up those irritating warning messages) and process it normally.

The transformation to +tlrc space makes the oblique issue moot.

Does that seem reasonable?

That is one of the options I plan to add to afni_proc.py, however
it is a low priority. The reason it is a low priority is that you
only transform the anatomy, so the processing of the EPI data is
unchanged. It is effectively outside the EPI processing stream.

But still, I will get a couple of options in there at some point...

- rick

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Subject Author Posted

3dWarp in Afni_proc.py

Steve Greening February 23, 2009 05:50PM

Re: 3dWarp in Afni_proc.py

rick reynolds February 23, 2009 06:17PM

Re: 3dWarp in Afni_proc.py

Steve Greening February 24, 2009 11:39AM