Thank you Andreas & Steve for your feedback!  This was very helpful.
--Ryan



On May 26 2010, Stephen Smith wrote:

> HI - yes this makes sense - thought I suspect that there probably isn't a 
> huge difference between working in a 'mid' space for the within-subject 
> affine registrations vs just taking one of the timepoints as a target, 
> given that probably the main advantage of doing a custom approach with 
> multiple timepoints will probably be the joint use (across all timepoints 
> wihtin-subject) of a single warp field.
>
>Cheers.
>
>
>On 25 May 2010, at 22:43, Andreas Bartsch wrote:
>
>> Hi,
>> 
>> what you could try is the following:
>> i) affinely register the individual FA maps to a template
>> ii) apply 'midtrans' to the 3 *.mat-files produced by flirt
>> iii) get the inverse using convert_xfm
>> iv) apply that to the template to get a midspace FA
>> 
>> You would then have to re-register the individual FAs and potentially 
>> average these prior to fnirting (to get a uniform non-linear reg across 
>> the 3 time points).
>> 
>> However, having said that I think even theoretically we have no 
>> "optimal" way or uniform gold standard to register longitudinal data 
>> yet. It all depends on the assumptions you are willing to make and the 
>> data you have. For example, if people were repositioned distortions may 
>> vary quite a bit. Then the best processing depends on the distortion 
>> correction and how good it works. Even signal loss can vary, e.g. you 
>> will observe less signal loss from adjacent sinuses if a subject comes 
>> in with sinusitis at one time point.
>> 
>> Essentially, you need to decide whether affine registration of the 
>> individual time points to each other for a given subject is really the 
>> way to go and at how many DOFs. But Steve has already indicated that the 
>> FMRIB crew is going into that.
>> 
>> Any comments, Steve / MJ / Jesper?
>> 
>> Cheers-
>> Andreas
>> 
>> ________________________________________
>> Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von 
>> Ryan Muetzel [[log in to unmask]]
>> Gesendet: Dienstag, 25. Mai 2010 22:05
>> An: [log in to unmask]
>> Betreff: [FSL] 3+ time point longidtudinal data
>> 
>> Hello,
>> 
>> We are conducting a longitudinal study and are using TBSS to warp each FA
>> map to standard space. With our DTI data, we've found slightly more
>> intra-subject variability in the nonlinear warp than we were expecting.
>> 
>> In an attempt to address this variability, prior to running tbss_2, we
>> align the time-1 and time-2 data into a half-way space (just as is done 
>> in
>> SIENA). From there, we compute an average FA map for each subject 
>> (time-1 +
>> time2/2) and feed that image into tbss_2 to determine the nonlinear warp.
>> We can then apply this warp to the individual time-point images using
>> tbss_non_FA. This method seems to reduce the intra-subject variability by
>> using the same nonlinear warp for each time point.
>> 
>> My question then is, is there a way to find the "mid point" among 3+ 
>> scans,
>> just as is done in SIENA with 2 scans?
>> 
>> Best,
>> 
>> Ryan
>
>
>---------------------------------------------------------------------------
>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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