Hi (forwarding this for Mark who's away),
Sorry for the delay in replying. This might be related to a buglet that
we fixed internally. Try using the latest version of mcflirt (for macosx
- is that right?) at:
http://www.fmrib.ox.ac.uk/fsldownloads/fsl-macosx-mcflirt
If that doesn't work, or you need a binary for another machine, let us
know.
All the best,
Mark
On Mon, 28 Apr 2003, Richard Albistegui-DuBois wrote:
> On Saturday, April 26, 2003, at 06:41 AM, Peter Bannister wrote:
>
> Sorry to bring this back up...I have been trying this, as you
> suggested, with no success. The output files from mcflirt are identical
> (compared with diff) to the input files. Here are the command lines I
> have been using:
>
> mcflirt -in AudMCor -out AudMCor_mcflirt20 -fov 20
>
> I've alse tried it with FOVs of 10 and 2, and with and without the -2d
> option. The program does not crash, but the output is identical to the
> input.
>
> These are 3-slice, 3mm thick/0 mm skip analyze 4d images. I know they
> have some motion (not a huge amount, but some) by visual inspection.
>
> Am I doing something wrong?
>
> Thanks again for your help, and your patience.
>
> -Richard
> > Dear Richard
> >
> > Apologies for the confusion arising from your use of mcflirt. The next
> > release includes a number of updates which we hope will make it easier
> > to process 2d/ small FOV data.
> >
> > Currently it is not possible to perform a restricted DOF correction
> > limited to in-plane movements only - mcflirt's approach (at present) is
> > to pad out thin or single-slice data and then treat it as 3d.
> >
> > In the interim I would suggest running mcflirt as normal but with the
> > -fov
> > 20 option. This will pad the input data to a volume whose fov in the
> > slice
> > direction is 2cm which may yield more satisfactory results.
> >
> > In any event, as this approach is somehwat heuristic, I would strongly
> > recommend inspecting the corrected data and playing around with the fov
> > parameter until you are satisfied with the results. We have managed to
> > "tune" the programme to handle motion-corrupted single-slice data
> > generated at FMRIB in a satisfactory manner by experimenting with fov
> > sizes.
> >
> > Hope this gives you something to work with
> >
> > regards,
> > Peter
> >
>
> Richard Albistegui-DuBois
> UCLA Brain Mapping
> 660 Charles Young Drive South, Room 237
> (310) 206-4456 phone
> (310) 794-7406 fax
> [log in to unmask]
> AIM: dubistegui
>
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