Hi Geoff -
No - nothing special - just the affine reg exactly as you describe.
T
On Tue, 19 Oct 2004, Geoff Parker wrote:
> Hi Tim,
>
> Does eddy_correct do anything special beyond the standard FLIRT affine
> registration of the diffusion weighted volumes to a b=0 volume?
>
> Geoff.
>
> > -----Original Message-----
> > From: FSL - FMRIB's Software Library
> > [mailto:[log in to unmask]] On Behalf Of Tim Behrens
> > Sent: 19 October 2004 14:18
> > To: [log in to unmask]
> > Subject: Re: [FSL] problems with FDT
> >
> >
> > Hiya -
> >
> > Yep we're aware of the negative x dimension problem with analyze
> > images. I think that all FSL programs write -ve x dimension
> > in analyze.
> > However, I would be surprised if this affects any future processing,
> > seeing as FSL programs also ignore the sign of the dimension.
> > (In fact, I
> > believe dtifit is completely ignorant of the data dimensions).
> >
> >
> > wrt eddy_correct, the effect that you are seeing is that
> > small rotations
> > needed for motion correction mean that there is no data left
> > in the parts
> > of the bottom or top slices.
> >
> > At the moment, these elements just have zeros placed in them
> > - however, I
> > think you're right that it would be better to pad with the
> > nearest piece
> > of "true" data. I have attached a replacement for the
> > eddy_correct script
> > which does this.
> >
> > if you download this file and do:
> >
> > mv eddy_correct ${FSLDIR}/bin
> > chmod a+x ${FSLDIR}/bin/eddy_correct
> >
> > Then, next time you run eddy correction you shouldn't see this effect.
> >
> > Cheers
> >
> > Tim
> >
> >
> >
> >
> >
> >
> >
> > On Mon, 18 Oct 2004, Erin Gibson wrote:
> >
> > > I'm running into a few problems with FDT. I've changed the
> > default save
> > > format to Analyze, but the headers do not appear to be
> > writing correctly.
> > > The data.img/hdr file created with eddy_correct has a
> > x-voxel dimension
> > > that is negative and if DTIfit is run on that file, the
> > results are just an
> > > empty volume. If I correct the header, DTIfit produces
> > reasonable output,
> > > but those files also have negative valued x dimensions.
> > >
> > > The second issue is with eddy_correct. After running the
> > correction on the
> > > 4-D data, the first slice on all images has missing data
> > and the exact
> > > amount missing differs across all the orientation and
> > baseline images. It
> > > almost looks like a rotation correction, but it only
> > affects the bottom and
> > > top slices. Could there be something that I am not doing properly?
> > >
> > > The input image (s1_4D.img/hdr) and output image
> > (data.img/hdr) can be found
> > > here:
> > > ftp://ftp.sunnybrook.utoronto.ca/pub/brainlab/fsl/
> > >
> >
> > --
> > --------------------------------------------------------------
> > -----------------
> > Tim Behrens
> > Centre for Functional MRI of the Brain
> > The John Radcliffe Hospital
> > Headley Way Oxford OX3 9DU
> > Oxford University
> > Work 01865 222782
> > Mobile 07980 884537
> > --------------------------------------------------------------
> > -----------------
> >
>
--
-------------------------------------------------------------------------------
Tim Behrens
Centre for Functional MRI of the Brain
The John Radcliffe Hospital
Headley Way Oxford OX3 9DU
Oxford University
Work 01865 222782
Mobile 07980 884537
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