Hi - you don't need to do any of this - SIENA does it for you! Just feed
in the original unprocessed images into SIENA and all should be fine.
Cheers, Steve.
On Tue, 16 Aug 2005, Jürgen Hänggi wrote:
> Dear FSL users
>
> I am a new FSL and SIENA user.
> I am investigating the brains of AD patients.
> I have data from two different time points.
> There are some questions concerning preprocessing of the data
> before applying SIENA:
>
> 1. I produced binary brain mask / segmented brain image / external skull
> surface image
> of all my MRI images (second and first) using BET
> 2. I registered the second brain image to the first brain image and applied
> the resulting transformations
> to the second skull image using FLIRT
> 3. I registered the transformed second skull image to the first skull image
> and applied the resulting
> transformations to the registered second brain image using FLIRT
> 4. Then I re-registered the resulting second brain image from 3. to the
> first brain image using FLIRT
>
> So far so good (are points 1-4 OK?), but now confusion arises
> In the FMRIB Technical Report TR00SMS1 (Measurement of Brain Change over
> Time)I have read that the above calculations resulting in two linear
> transformations from which one have to be applied to the first input
> image and the other to the second input image.
> My questions are:
>
> Which transformation have to be applied to which image and how to do this?
> Actually, I have four time points and not only two. Is there a paper or
> manual
> that describes the SIENA procedure with more than two time points?
>
> Thanks a lot in advance
> Best regards
> Juergen
>
>
> ----------------------------------------------
> Juergen Haenggi, Ph.D. student
> Division of Psychiatry Research
> Psychiatric University Hospital
> University of Zurich, Switzerland
> P.O. Box 1931
> Lenggstrasse 31, 8032 Zurich
> 0041 44 384 26 10 (office phone)
> 0041 76 445 86 84 (mobile phone)
> 0041 44 384 26 86 (fax)
> H 115 (office room number)
> [log in to unmask] (division email)
> http://www.dpr.unizh.ch/ (division website)
> http://www.juergenhaenggi.ch (private website)
> ----------------------------------------------
>
>
--
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe 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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