Hi - given that this data is quite different from the FMRI data for which
mcflirt was optimised, you are probably better off using FLIRT, which is a
more general program. You should be able to get good registration with
FLIRT, and will need a simple script to split the 4D data up into 3D
images, run flirt on each, and recombine (avwsplit & avwmerge).
Good luck! Steve.
On Wed, 5 May 2004, Johannes Klein wrote:
> Hi Mark,
> thanks for your advice! No, I'm running Linux. I'm currently trying to find
> a parameter set that allows realignment of multi-frame F-DOPA scans.
> Unfortunately, the results I've obtained so far are not convincing. I've
> compared them to SPM's results and there is some motion that is quite
> visible when I scroll through the time series using FSLview, which is not
> present after realignment with SPM.
> Now, I'm trying to find out how to opimize the whole process, so I can get
> the same results using mcflirt. I've tried all of the available cost
> functions (except for normmi), setting -smooth 0.0 (in my DOPA frames, the
> scalp shows up nicely, but is naturally closer to the border of the FOV than
> the other brain structures, so I thought deweighting peripheral voxels might
> hinder correct registration), and setting -stages 4. Unfortunately, these
> changes did not produce satisfactory results.
> Do you have any further suggestions how I should proceed? I understand that
> PET frames are quite different from an fMRI time series, but I hope there's
> a way to make mcflirt work for this.
> > -----Ursprüngliche Nachricht-----
> > Von: FSL - FMRIB's Software Library
> > [mailto:[log in to unmask]] Im Auftrag von Mark Jenkinson
> > Gesendet: Mittwoch, 5. Mai 2004 09:10
> > An: [log in to unmask]
> > Betreff: Re: [FSL] mcflirt exception
> > Hi,
> > Are you using cygwin?
> > It may be a problem with that binary - we could not replicate
> > the previous problem that Thomas had.
> > However, I think it went away for Thomas if he stopped using
> > the -meanvol option. In general we do not recommend using
> > the -meanvol as we have done tests (see Jenkinson, M.,
> > Bannister, P., Brady, J. M. and Smith, S. M., Improved
> > Optimisation for the Robust and Accurate Linear Registration
> > and Motion Correction of Brain Images/, NeuroImage/, 17(2),
> > 825-841, 2002.) and meanvol doesn't turn out to be the best.
> > It isn't far off but it does degrade the results. Partly
> > this is because the initial mean is not made from well
> > registered volumes, but partly it is because the mean is
> > inevitably smoother than an individual volume which means
> > that it is a better match if the registration smooths the
> > original volume by adding some offset and making the
> > interpolation do some smoothing. This is why we use a single
> > volume reference in FEAT.
> > So, try it without the meanvol and see if it works.
> > All the best,
> > Mark
> > On Tuesday, May 4, 2004, at 02:26 pm, Johannes Klein wrote:
> > > Hi everybody,
> > > I've come across a problem that is similar to the one
> > Thomas Mierdorf
> > > had posted previously. I'm trying to realign a series of PET frames
> > > using mcflirt and the -meanvol and -plots option, which
> > results in an
> > > "Image Exception : #5 :: Out of Bounds (time index)" error in the
> > > final iteration
> > > of the second, realign-to-mean process.
> > > The command line is:
> > > mcflirt -report -plots -meanvol -in filename -out filename_mcf
> > > If I don't use the -plots option, everything works, but I'd really
> > > like to
> > > be able to check how much patient movement there is in my
> > time series.
> > > It seems like there's a problem with the generation of the
> > > transformation
> > > parameters file.
> > > The output of avwhd, avwstats -r -R can be found at
> > > http://www.mpifnf.de/~johannes/mcflirterror.txt
> > > I'd appreciate any help with this!
> > > Thanks
> > > Johannes
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