hi - you could try the intermediate release binaries in
www.fmrib.ox.ac.uk/~jim - otherwise there'll be a next release sometime in
the summer.
cheers.
On Mon, 7 Jun 2004, Fornito, Alexander wrote:
> That does help - thanks!
> Another question - We've been unable to get FSLview working from either
> the GUI or command line (All the other FSL programs work fine). The
> error message reads:
> .../fslview_bin: error while loading shared libraries: libssl.so.2:
> cannot open object file: No such file or directory
>
> We are running Linux Debian (Woody) on Dual AMD athalon processors.
>
> Thanks again!
> Alex
>
>
> -----Original Message-----
> From: Mark Jenkinson [mailto:[log in to unmask]]
> Sent: Sunday, June 06, 2004 9:07 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Registration for fMRI analysis
>
> Hi Alex,
>
> If you have a lot of neck in your images then BET doesn't work
> well unless you either truncate the images to remove most of
> the neck (using avwrio for instance), or select the coordinate
> of the centre of the brain (using FSLView for instance) and
> specify this with the -c option in BET. Note that little bits of
> non-brain tissue are fine but substantial amounts do affect
> the registration.
>
> As for registration error - it depends on what images you are
> registering. For EPI to structural in the same individual, you
> expect to get within 0-2mm for most areas in a reasonable
> registration (remember that your EPI voxels are often 4mm)
> but this gets worse if you have substantial B0 (susceptibility)
> distortion. For structural to standard space, that is much harder
> and because of population variability the result depends a
> lot on the area and how "normal" the individual was. Again
> 0-2mm would be a good registration, but around the ventricles
> it may be more than this. Of course all of this is specific to
> affine registration to standard space (the only option in FSL
> currently).
>
> Hope this answers your questions.
> All the best,
> Mark
>
>
>
> On Wednesday, June 2, 2004, at 08:34 am, Alex Fornito wrote:
>
> > Hi all,
> > I'm a first time fMR researcher and FSL user.
> > Just had a couple of questions re: registration as implemented in
> FEAT.
> >
> > 1. I'm following the recommedations to register the epi to the
> template
> > via the hi-res structural. How well stripped (using BET) does the
> > structural have to be? I am often left with residual bits of non-brain
> > tissue (especially neck) and I was wandering whether this would
> greatly
> > affect the registration results for my purposes (ie., epi to
> template).
> > Would manually removing non-brain tissue be worthwhile? (playing with
> > FIT
> > and g still doesn't yield great results in many cases, unless I'm
> > doing it
> > wrong?)
> >
> > 2. Are there any rules of thumb re: determining what's a minimally
> > acceptable registration? Are minor deviations around the edges ok,
> > provided there isn't evidence of gross misalignment? How large would
> > these
> > minor deviations have to be before they are considered problematic?
> Are
> > there any examples of bad, or (just) decent registrations on your
> > website?
> >
> > Many thanks for your help - am enjoying the software!
> > Alex
>
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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