Hi Mark,
I had a problem in header. I didn't pay attention to dim4 while generating
header for that file. After I corrected it, all went pretty smoothly. Many
thanks for help.
Martin
On Thursday 10 October 2002 07:21, Mark Jenkinson wrote:
> Dear Martin,
>
> Flirt now transforms 4D images when the -applyxfm option is specified, so
> if your image CBVu_256 does not have the number of time points correctly
> specified in the header then this could cause the problem. The previous
> version only ever read in the first volume and applied the transform to
> that, so it wouldn't care about the setting of dim4 in the header.
>
> To see if this is the case run:
> avwhd CBVu_256
> and see what the value for dim4 is.
> If it is incorrect then it needs to be fixed (try avwcreatehd)
> Otherwise it will be some other problem, in which case please make some
> arrangement to send me the data (don't send it to the list) and I'll have
> a look.
>
> All the best,
> Mark
>
> Martin Kavec wrote:
> > Hello everybody,
> >
> > I am experiencing problems with flirt (FSL3) that I didn't have with
> > previous version.
> >
> > This is what I do:
> >
> > flirt -in stack.hdr -ref ../../T1/T1_brain_to_T2_flirt.hdr -out
> > stack_flirt.hdr -omat stack_flirt.mat -bins 256 -cost corratio -searchrx
> > 0 0 -searchry 0 0 -searchrz 0 0 -dof 12 -interp trilinear -paddingsize 1
> >
> > and after that
> >
> > flirt -in CBVu_256 -ref ../../T1/T1_brain_to_T2_flirt -out
> > CBVu_256_flirt -applyxfm -init stack_flirt.mat -paddingsize 1
> >
> > The last command, however fails saying
> >
> > Image Exception : #5 :: Out of Bounds (time index)
> > Aborted
> >
> > Does anyone have an idea what's going on.
> >
> > Thanks in advance for help,
> >
> > Martin
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