Good morning,
Just to add to Steve's response:
If you have, for example, acquired your data at a matrix of 512 but only sample a matrix of 256 you're effective resolution is FoV / 256 but some conversion routines will "pretend" that you have sampled by FoV / 512. I think it is possible that you have in fact sampled a resolution of ~ 1mm in plane but that due to the above the analyze or whatever format files are stored at ~ 0.5mm in-plane resolution. Are you, by any chance, using SPM's DICOM toolbox to convert Siemens data? What does avwinfo tell you?
Cheers-
Andreas
-----Ursprüngliche Nachricht-----
Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag von Stephen Smith
Gesendet: Montag, 6. Juni 2005 10:22
An: [log in to unmask]
Betreff: Re: [FSL] FLIRT trouble
Hi - I just ran FLIRT with the default settings - ie 12 DOF and normal search, and the epi->T1 registration ran fine. Your T1 does have the x and y voxel dimensions < 0.5mm which does probably mean that you're getting bitten by that old bug - I think this was patched in one of the patch releases after the original 3.2b FSL release, so you can either get this by taking the latest patch or just re-downloading FSL.
Cheers, Steve.
On Mon, 6 Jun 2005, Cornelius Werner wrote:
> Hello Steve,
>
> thanks for your effort! I don't think my T1's are of very high
> resolution - we usually do not have enough time for that :-) Besides,
> I'm pretty sure I used the most recent version of FSL. Does FLIRT
> depend on any external libraries that might not be in order?
> Anyway: could you be so kind to tell me which parameters you provided
> FLIRT with (or send me the log-file)? That would be greatly
> appreciated.
>
> Cheers
> Cornelius
>
>
> On Sat, 2005-06-04 at 11:23 +0100, Stephen Smith wrote:
> > Hi Cornelius, thanks for sending the data. Registering
> > example_func01 to
> > T1_bet_struct01 works fine for me - I think what's going on for you is an
> > old FLIRT bug when one of the images is of very high resolution (<.5mm in
> > any direction). If you take the latest FSL (or patch) download hopefully
> > all should be ok.
> >
> > The patches are available from:
> > http://www.fmrib.ox.ac.uk/fsldownloads/patches/3.2/
> >
> > Cheers, Steve.
> >
> >
> > On Fri, 3 Jun 2005, Cornelius Werner wrote:
> >
> > > Hello all,
> > >
> > > I know, I posted this problem some time ago, but I am still having
> > > problems with my T1 structurals. Neither can I register my EPIs
> > > onto them, nor can I register the structurals to any template
> > > image (avg152, colin27, whatever). Thus, I'm stuck with
> > > registering my EPIs directly onto standard brains, which is far
> > > from optimal. The problem is that FLIRTing to/from structurals
> > > results in considerable offsets in all directions. Can this be due
> > > to the origin in the structurals not being AC?
> > >
> > > I created the structurals as follows:
> > >
> > > SIEMENS Sonata DICOMs -> xmedcon -> ANALYZE -> avwchfiletype ->
> > > NIFTI.GZ
> > > -> Bet -> skull stripped structurals.
> > >
> > > In FSLView, they look ok, however...!
> > >
> > > Does anyone else also suffer from this problem? Anyone having a
> > > solution?
> > >
> >
>
--
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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