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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Dxc536
September 04, 2019 03:05PM
Hello,

I have two fMRI runs that I'm analyzing using afni proc. I've noticed in some instances the EPI's of the two runs are not aligned with eachother. Also, I have been using Align Anat2Epi, which means the two EPI's remain in non-warped form.

What's odd to me, is that after looking the stats, the results don't look all that bad (i.e. the activation is where I would expect it to be despite one of the EPI's being completely unaligned to the other EPI).

Since I have two fMRI runs, is it more appropriate to align them both to Anat so they are aligned properly when being analyzed, or is AFNI_proc already aligning the two EPI's together? I can' find any commands that would suggest the latter...

Also, is there a way to use Afni_proc.py and align epi2anat without a volreg input? I've been using Slice motion correction (SLOMOCO) for my motion correction and I was advised not to run 3dvolreg on the data after I run SLOMOCO. Should I just use align_epi_anat.py with -epi2ant and then run the output through afni_proc.py with the align and volreg blocks?

Thanks for your help



Edited 4 time(s). Last edit at 09/04/2019 05:02PM by Dxc536.
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Align 2 fMRI runs?

Dxc536 September 04, 2019 03:05PM