Great to hear! :)
Happy holidays.
All the best,
Niels
On Dec 27, 2007 6:34 PM, Steve Smith <[log in to unmask]> wrote:
> Hi - yes, sorry about that. This was due to a 'feature' in our options
> parser. We've now fixed this, and this will get included in the next
> patch release very soon.
> Cheers, Steve.
>
>
>
> On 17 Dec 2007, at 16:00, Niels Bergsland wrote:
>
> > Hi,
> > Sorry if this has been posted previously. I did however search the
> > list so
> > I don't think it has! :)
> >
> > The basic problem: bet2 completely ignores a given option if it is
> > passed twice.
> >
> > Background information:
> > I initially found the error by running sienax with -B "-t -S" which
> > caused
> > SIENAX to fail with several errors.
> > For example:
> >
> > ** ERROR (nifti_image_read): failed to find header file for
> > 'I_brain_tmp_premask_bet_mask'
> >
> > Upon further investigation, I found on line 177 of the SIENAX script:
> > ${FSLDIR}/bin/bet $I ${I}_brain -s -m $betopts
> >
> > The problem first arises on line 262 of the bet script:
> >
> > ${FSLDIR}/bin/bet2 $IN ${OUT}_tmp_betraw -s $bet2opts
> >
> > The issue is that when bet2 is passed the same option twice, (in
> > this case,
> > -s) it ignores the option all together.
> >
> > The same behavior is exhibited on line 266 of bet with the -m option
> > being
> > passed twice. (It is already part of the bet script, and also being
> > passed
> > in from $betopts).
> >
> > The behavior can be confirmed by taking a sample input and running
> > bet2 with
> > no options, then running it with the same option twice. A diff of
> > the files
> > will show that they are identical.
> >
> > I know that this is a bit long winded, but I wanted to give as much
> > detail
> > as possible so that you can recreate the problem.
> > Regards,
> > Niels Bergsland
> >
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
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