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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Peter Molfese
April 17, 2015 11:40AM
Hello,

Using 3dWarp and align_epi_anat.py shouldn't put everything into common space. AFNI uses the +tlrc to signify ANY common space (MNI, TLRC, HaskinsPediatric, etc). It could be that one of your anatomical files is incorrectly reporting the space that it is in and that may be causing a problem. Also, you shouldn't have to deoblique the data before alignment, align_epi_anat.py should do this for you. Let's start with these three questions:

1) What is your original align_epi_anat.py command?
2) What is the output of afni_system_check.py -check_all
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Subject Author Posted

Deoblique and maintain +orig space

rnauer April 17, 2015 11:21AM

Re: Deoblique and maintain +orig space

Peter Molfese April 17, 2015 11:40AM

Re: Deoblique and maintain +orig space

rnauer April 17, 2015 12:18PM

Re: Deoblique and maintain +orig space

Peter Molfese April 17, 2015 12:47PM