Hi there -
the problem here is that you are working in the FEEDS original data +
example/test output data directory - so the output from this command
already exists hence the error messages...
In general you shouldn't run FSL programs in the FEEDS data directory -
otherwise you won't be able to run FEEDS reliably in the future! All you
have to do to test bedpost in this way is to make a copy of the fdt_subj1
directory somewhere else first and use that.
Cheers,
T
On Wed, 2 Nov 2005, willcott wrote:
> Hi Tim-
> Here is my scope.
> 1. Mac OS 10.4.2 (Tiger).
> 2. I have no file diff_slices anywhere on my system.
> 3. The only log file with contents is a reference to Log
> directory was: /home/fs3/steve/fsl_dev/src/feeds3.2/data/
> fdt_subj1.bedpost/diff_slices/data_slice_0000.
> 4. bc returns bc 1.06 (I run in bash shell)
>
> Thanks in advance.
> Bob
>
>
> On Nov 2, 2005, at 1:37 AM, Tim Behrens wrote:
>
> > Hi - can you tell me a few things.
> > 1) what operating system are you running (e.g. Linux, cygwin etc.)
> > 2) what are the contents of the directory fdt_subj1.bedpost/
> > diff_slices
> > 2) what are the contents of the directory fdt_subj1.bedpost/logs
> > 3) do you have a program called bc
> > (i.e. if you type bc into a shell, what happens)
> >
> > Thanks
> >
> > T
> >
> > On Tue, 1 Nov 2005, M. Robert willcott wrote:
> >
> >
> >> Hello bedpost users,
> >> I am a recent convert to DTI and have been trying to run
> >> bedpost on
> >> the sample data from the fsl website. I get an error that I would
> >> like
> >> some help with please. The output is as follows.
> >>
> >> /Desktop/feeds/data willcott$ sudo bedpost fdt_subj1
> >> Password:
> >> subjectdir is /Users/willcott/Desktop/feeds/data/fdt_subj1
> >> making bedpost directory
> >> copying files to bedpost directory
> >> processing data on local host
> >> Merging outputs into 4D files
> >>
> >> Usage: avwmerge <-x/y/z/t> <output> <file1 file2 .......>
> >>
> >> -t : concatenate images in time
> >> -x : concatenate images in the x direction
> >> -y : concatenate images in the y direction
> >> -z : concatenate images in the z direction
> >>
> >> -a : auto-choose: single slices -> volume, volumes -> 4D (time
> >> series)
> >>
> >>
> >> Usage: avwmerge <-x/y/z/t> <output> <file1 file2 .......>
> >>
> >> -t : concatenate images in time
> >> -x : concatenate images in the x direction
> >> -y : concatenate images in the y direction
> >> -z : concatenate images in the z direction
> >>
> >> -a : auto-choose: single slices -> volume, volumes -> 4D (time
> >> series)
> >>
> >>
> >> Usage: avwmerge <-x/y/z/t> <output> <file1 file2 .......>
> >>
> >> -t : concatenate images in time
> >> -x : concatenate images in the x direction
> >> -y : concatenate images in the y direction
> >> -z : concatenate images in the z direction
> >>
> >> -a : auto-choose: single slices -> volume, volumes -> 4D (time
> >> series)
> >>
> >> DONE
> >> /usr/local/fsl/bin/bedpost: line 293: syntax error: unexpected end of
> >> file
> >>
> >>
> >>
> >>
> >>
> >
> > --
> > ----------------------------------------------------------------------
> > ---------
> > 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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