I have a question about the realignment parameters saved after
performing "Realign and Unwarp" with SPM5.

I realigned two sessions (i.e., scan runs) using the default setting
with the first image of the first session as the reference image. I
performed realignment in two ways:

Method 1: Included all the volumes in both sessions.

Method 2: Included only the first volume for the first session (Session
1), but all the volumes in the second session (Session 2).

I was expecting the realignment parameters for Session 2 to be identical
or near identical with both realignment methods. However, this is not
what I got (see attached image). With Method 1, the realignment
parameters for the first volume (row 1 in the upper table of the
attached image) are almost all 0s except for the second column. But,
with Method 2, the realignment parameters for the first volume (row 1 in
the lower table in the image) are quite different from the results of
Method 1, although the rest looked almost identical. Why is there such a
difference for volume 1? Is it expected? 

Thanks much for your help.


-----Original Message-----
From: John Ashburner [mailto:[log in to unmask]] 
Sent: Tuesday, March 24, 2009 1:57 PM
To: [log in to unmask]
Subject: Re: [SPM] Dartel Normalization of fMRI data

If you have SPM8b (latest updates), then you should find this much
easier, as there is now an option to spatially normalise (and spatially
blur) fMRI to MNI space (as it incorporates an additional affine mapping
between DARTEL template and MNI template).  I haven't had a chance to
update the user guide for DARTEL yet, but it should be reasonably
straightforward to use.

I expect that the t stats should be increased, and look forward to any
feedback on whether this is the case.

Best regards,

On Tuesday 24 March 2009 16:22, Amir Tahmasebi wrote:
> Dear John and SPMers,
> I am trying to use DARTEL for normalization of fMRI data. I have 
> looked at "how to use DARTEL for normalizing fMRI con maps?" thread 
> but it is not exactly what I was looking for.
> I was wondering how should I use the outputs of DARTEL ("u_rc1*.nii" 
> and
> "Template_6.nii") to normalize my fMRI data which is already 
> coregistered to the corresponding structural data.
> Thank you,
> Amir