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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sungshinkim
September 02, 2018 11:40PM
AFNI experts,

I used Multi-Band Accelerated EPI Pulse Sequences, so-called CMRR protocol.
TR = 460 ms, voxel size = 2.7 mm

When I used this protocol, additional 4 images for distortion corrections (two for each of polarity, A->P or P->A) were acquired before actual fMRI scanning.
Also, for each run, there were additional reference images.
I heard that I can use FSL function, "topup" for correcting distortion using the four images.
Also, I heard that for each run, I can use the reference image when I perform motion correction.

Is there any AFNI script for this procedure of preprocessing?
I don't know how to use these additional images in addition to conventional AFNI preprocessing (guided by afni_proc.py)
Thank you in advance.



Sincerely,
Sungshin Kim
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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