Hi - this depends on whether you want to align the functional scans to
each other and to the structurals before doing whatever analysis it is you
are going to do. You should run MCFLIRT before running BET on the
functional data. You can use the FLIRT GUI to get all relevant transforms
and the FLIRT->utils to concatenate and apply the transforms, including
applying to 4D data.
Hope that's enough! Cheers, Steve.
On Tue, 27 Dec 2005, Steven Bradley Lowen wrote:
> I have two low-resolution functional scans and one high-resolution anatomic
> scan, all acquired on the same subject within two hours of each other, and
> I'd like to align them. My analysis isn't GLM or ICA, so I'd like to
> perform the alignment outside of FEAT. Currently, I'm trying the following:
> 1) run BET on all three scans
> 2) use FLIRT to align each functional scan to the anatomic as reference,
> with 12 DOF, saving the resulting matrices (but not generating output data sets)
> 3) run MCFLIRT on each functional scan, using the -init option to include
> the associated matrix generated by FLIRT
>
> I have three questions:
> 1) Is this the right way to proceed?
> 2) Which volume does FLIRT choose when it performs the alignment to the
> structural image?
> 3) Should I run BET before FLIRT and MCFLIRT, or after? Message #6302 seems
> to suggest that in this case perhaps not.
>
> Many thanks for a great suite of programs.
>
> Steve
> http://cordelia.mclean.org/~lowen/
>
--
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, 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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