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Subject:

Re: how to analyze data with variable slice durations resulting from volume-selective z-shim compensation

From:

Torben Ellegaard Lund <[log in to unmask]>

Reply-To:

Torben Ellegaard Lund <[log in to unmask]>

Date:

Thu, 8 Jan 2009 13:21:09 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (65 lines)

Dear Stephan

This is an interesting problem, which I have been speculating about  
for some time now. I guess the slice timing procedure could be  
modified, but as we discussed earlier today slice specific  
designmatrices would be a better solution. As a workaround you could  
include a the hrf time derivative, this can account for small  
differences in arrival of the hrf. Note that while the individual  
slices take a different amount of time to acquire, the repetition time  
is the same for all slices.

Hope this helps

Torben

Torben Ellegaard Lund
Assistant Professor, PhD
The Danish National Research Foundation's Center of Functionally  
Integrative Neuroscience (CFIN)
Aarhus University
Aarhus University Hospital
Building 30
Noerrebrogade
8000 Aarhus C
Denmark
Phone: +4589494380
Fax: +4589494400
http://www.cfin.au.dk
[log in to unmask]



Den 10/12/2008 kl. 18.06 skrev stephan hamann:

> We're testing an in-house sequence that applies z-shim compensations  
> only to selected slices, similar to what Du et al. (2007; MRM) have  
> used. The idea is to recover signal from OFC and amygdala without  
> increasing the overall TR markedly, by just applying the z-shim to  
> the areas most affected by artifacts.
>
> However, this now results in some slices having a slightly longer  
> acquisition time than others, for example, inferior axial slices  
> take 100 msec to acquire, whereas superior slices take only 66 msec  
> to acquire (sequence is interleaved on the Trio).
>
> It isn't clear how to do slice-timing with unequal slice acquisition  
> times, or what other problems this may introduce -- all of the SPM  
> documentation seems to assume equal slice durations, yet it would  
> seem possible to modify this in the slice-timing routine.
>
> Has anyone encountered this sort of issue before?
>
> Thanks,
> Stephan
>
>
>
>
>
> Stephan Hamann
> Department of Psychology
>
> email: [log in to unmask]
> http://www.socialtext.net/hamannlab

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