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
September 04, 2018 08:49AM
Hi Sungshin,

We refer to those 2 pairs of distortion correction images as forward and reverse blip datasets. The forward direction should match that of the functional EPI data, while the reverse is the opposite.

Those 2 datasets can be passed to afni_proc.py using -blip options:
-blip_forward_dset FORWARD+orig \
-blip_reverse_dset REVERSE+orig \


The resulting proc script will have a 'blip' processing block, which you are welcomed to review.


There is no option to apply per-run reference images (except to pre-process using multiple afni_proc.py commands). If shimmimg was applied between runs, it would be a good idea to use per-run registration. Otherwise, it is unlikely to matter much.

- rick
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Preprocessing data acquired using CMRR protocol

sungshinkim September 02, 2018 11:40PM

Re: Preprocessing data acquired using CMRR protocol

rick reynolds September 04, 2018 08:49AM