That's right - we found originally that _in general_ the single middle  
image is sharper than an average image - so you get more precise  
motion correction.
Cheers.

On 2 Jun 2009, at 03:04, David V. Smith wrote:

> I believe that’s what you should expect, so I don’t think you’re  
> doing anything wrong. However, you might find the default option of  
> the middle volume—rather than an average volume based on the raw data 
> —a little more precise when correcting for motion. Maybe some of the  
> experts can chime in if this intuition is wrong…
>
> Cheers,
> David
>
>
>
>
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On  
> Behalf Of Zarrar Shehzad
> Sent: Monday, June 01, 2009 9:34 PM
> To: [log in to unmask]
> Subject: Re: [FSL] AW: [FSL] FSL-MotionCorrection
>
> Hi,
>
> Another follow-up question about fsl_motion_outliers. I usually use  
> the average functional image as my reference for motion correction.  
> I changed the fsl_motion_outliers script to use this mean functional  
> image for motion correction and to generate the residual mean square  
> error. However, I got different results for the spikes if I used  
> this approach versus the standard approach in the script (ie using  
> the middle image of the run). I also got different result if I used  
> a different reference time point. Is there something that I am doing  
> wrong?
>
> Thanks!
> Zarrar
>
> On Wed, May 27, 2009 at 2:00 PM, Mark Jenkinson  
> <[log in to unmask]> wrote:
> Hi,
>
> No need to do anything like this.
> FEAT has always been able to handle different design matrices
> for different first-level analysis - including different numbers of
> EVs.  As long as you don't want any of these to enter any contrasts
> (and you can't really with the confound set-up) then there is
> no problem at the first or any higher-level analysis.
>
> All the best,
>        Mark
>
>
>
> On 27 May 2009, at 21:12, Andreas Bartsch wrote:
>
> Hi,
>
> just a follow-up question: fsl_motion_outliers is likely to generate  
> a different number of confound EVs  for every subject. Prior to  
> higher level analyses, would we be expected to fill up confounding  
> outlier EVs of every subject exhibiting less than the maximum  
> outliers by dummy EVs so that every first level design matrix  
> contains the same total number of EVs (keeping the DoFs constant  
> across subjects)? Does that pertain to fixed as well as mixed effect  
> analyses, and also to OLS vs. FLAME?
> Cheers-
> Andreas
>
> ________________________________________
> Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag  
> von Jesper Andersson [[log in to unmask]]
> Gesendet: Donnerstag, 21. Mai 2009 20:21
> An: [log in to unmask]
> Betreff: Re: [FSL] FSL-MotionCorrection
>
> Dear Zarrar,
>
> I was interested in doing something just like this and was glad to
> see that Klara asked this question. I have another clarification
> question regarding the use of fsl_motion_outliers. When you add the
> confound file produced by fsl_motion_outliers to your FEAT model,
> does this impact the inclusion of the motion parameters as
> covariates? So if you previously included the motion parameters as
> covariates, will they no longer be necessary with the inclusion of
> the confound matrix from fsl_motion_outliers?
>
> No, they are pretty much complementary. Including the motion
> parameters removes (as a first order approximation) effects that
> depend ~linearly on subject position, such as e.g. distortion-by-
> position and dropout-by-position interactions.
>
> The covariates you get from motion_outliers on the other hand removes
> effects related to "subject velocity" (again as a first order
> approximation). For example if someone makes a sudden movement in the
> middle of the acquisition of a volume the rigid-body transformation is
> no longer valid, and such a volume would be picked up by
> motion_outliers.
>
> Good Luck Jesper
>


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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
[log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
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