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
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,
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
> 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
> 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
> parameters file.
> The output of avwhd, avwstats -r -R can be found at
> I'd appreciate any help with this!