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
>
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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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