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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Danny
July 02, 2014 12:35PM
Hi AFNI experts,

I was wondering if there is a "best" point during preprocessing to do the registration to a standard template? I know some programs do it before subject-level statistics, while others do it after.

I am currently running everything within AFNI_proc.py. I am wondering if I can do all the preprocessing (e.g., motion & slice-time correction, blurring, convert to mean % signal change, etc.) using proc.py, then do registration in a separate script (Qwarp or FSL's FNIRT). Then run 3dDeconvolve after registration. Will this be appropriate?

The reason I plan to do the registration outside of proc.py is that for our dataset, Qwarp is not doing a great job in proc.py. I either plan to see if the @toMNI_Qwarp option (or FNIRT) will work better for registration and then apply it to the EPI data.

Thanks,

Danny
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Subject Author Posted

When to do registration

Danny July 02, 2014 12:35PM

Re: When to do registration

nick July 03, 2014 06:46AM

Re: When to do registration

Danny July 03, 2014 10:13AM