Dear Carol,
At the moment FABBER doesn't deal with registration at all. It's
simply a drop-in replacement for the GLM (or the nonlinear least
squares fitting) that is normally used in dual-echo ASL analysis.
Motion correction on this type of data is tricky, and might do more
harm than good. I'd suggest starting with data from a single echo
time and running MCFLIRT on that. If it looks like the tag-control
signal is leaking into the motion regressors, you may need to try
again using only the control volumes. For the volumes you left out,
it's probably best to simply re-use the transformations from the first
MCFLIRT.
To remove the residual motion signal, you should also pass the motion
regressors into FABBER using the
"--nuisance-basis=your_motion_regressors.mat" option.
Thanks for the question, and let me know how you get on.
Cheers,
Adrian Groves
DPhil Student in Oxford Centre for Functional MRI of the Brain (FMRIB)
Dept of Clinical Neurology, University of Oxford
> From: "Dr. Carol Docherty" <[log in to unmask]>
> Date: 11 March 2008 13:31:37 GMT
> To: [log in to unmask]
> Subject: [FSL] ASL timeseries realignment
> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>
> Dear FSL'ers,
>
> I have been looking into the new FABBER toolbox in FSL, and was
> wondering how the package handles the registration of a multi-echo
> multi-inflow time-series given how much the image contrast varies
> with these parameters? How might you suggest registering such a
> timeseries?
>
> Thanks,
> Carol
> --
> Dr Carol Docherty
> Postdoctoral MRI Scientist
> Department of Neurophysics
> Max-Planck Institute for Human Cognitive and Brain Sciences
> Stephanstraße 1A
> 04103 Leipzig
> Germany
>
> Tel: +49 (0)341 99 40 291
> Fax: +49 (0)341 99 40 221
> Email: [log in to unmask]
>
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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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--
Adrian Groves
+44 7722 145278
[log in to unmask]
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