The usual is coregister T1 on mean in your batch but the 1st step could be coregister T1 on template, and apply to epi. Of course the coregistration will be bad as t1 and template are not in the same space but by trying to align them the t1 origin will be moved at the right place :-) then carry on as usual
There is also a utility to reorient see batch tools, you can batch this and call iteratively, giving an approximate location for AC.
Sent from my mobile phone
Dr Cyril Pernet
Brain Research Imaging Centre
www.sbirc.ed.ac.uk/cyril/
----- Reply message -----
From: "Jie Yu" <[log in to unmask]>
To: <[log in to unmask]>, "Dr Cyril Pernet" <[log in to unmask]>
Subject: Re-orient before fMRI analysis in SPM8
Date: Fri, Jul 12, 2013 09:43
Hi Cyril
Thanks for your reply!
I have already included 'coregister' in my batch pipelines.
ButI do I always have to MANUALLY 're-orient' the MRI image before actually running the batch?
( Most of my MRI images have origins far away from the anterior commissure )
Thank!
