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

History of AFNI updates  

Previous Message Next Message
Message List New Topic Print View
|
rick reynolds
December 09, 2019 05:16PM
Hello,

Sorry for being so slow on this.

You mention is one volume of AP direction map and one volume of PA direction map for each run of the epi images. Those are opposite phase directions, they are not B0 distortion maps.

What we do in this case is to non-linearly register the forward direction (PA?) with the reverse direction (AP?) map, and then take the "midpoint" or the sqrt(xform). That can be done easily in afni_proc.py, but providing one pair of those images using -blip_forward_dset and -blip_reverse_dset. Very easy.

The difficulty here would be doing this per run. Right now, afni_proc.py is only able to do this once across all runs. You could work around this limitation by running AP per run, maybe giving it the first run's volreg base for the rest to align to, or you could just use the first pair only.

I will ponder this going forward.

- rick
Reply Quote
RSS
Subject Author Posted

b0 field map distortion correction Attachments

zjjdcrn November 19, 2019 12:07PM

Re: b0 field map distortion correction

rick reynolds December 09, 2019 05:16PM