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
|