I'm on fsl 5.0.2 and Ubuntu 10.04.
I run bet with all options withouth problems, but when I run siena/sienax with betopt -B "-f ...." (i.e. siena input1 input2 -B "-f 0.3"), it appear this message on terminal:
Usage: siena <input1> <input2> [options]
-o <output-dir> : set output directory (default output is <input1>_to_<input2>_siena)
-d : debug (don't delete intermediate files)
-B "betopts" : options to pass to BET brain extraction (inside double-quotes), e.g. -B "-f 0.3"
-2 : two-class segmentation (don't segment grey and white matter separately)
-t2 : T2-weighted input image (default T1-weighted)
-m : use standard-space masking as well as BET
-t <t> : ignore from t (mm) upwards in MNI152/Talairach space
-b <b> : ignore from b (mm) downwards in MNI152/Talairach space (b should probably be negative)
-S "sienadiffopts" : options to pass to siena_diff timepoint differencing (inside double-quotes), e.g. -S "-s -i 20"
-V : run ventricle analysis (VIENA)
-v <mask image> : optional user-supplied ventricle mask (default is /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_VentricleMask)
This message don't appear with all other options (also "betops") and siena/sienax run correctly.
Thanks in advance for any helping.