[Neurodebian-users] SienaX doesn't accept options

[Lorenzo Bandieri]

Hi list,

I'm using FSL 5.0. I'm trying to pass SienaX (fsl5.0-sienax) an
option; according to the documentation[1], it should be possible to
pass the optional parameter -B to change the BET defaults, e.g

fsl5.0-sienax foo_bar -B "-f 0.3"

In my case, every attempt to pass a value with the -B option has been
unsuccessful. Running sienax as in the example above returns
immediately the message "Usage: sienax <input> [options] etc etc" (as
if I'm not using it correctly).

Interestingly, if I run:

fsl5.0-sienax foo_bar -B ""

I get a meaningful error message:

/usr/share/fsl/5.0/bin/sienax: 121: shift: can't shift that many

Furthermore, running

fsl5.0-sienax foo_bar -B "-f"

Similarly seem to return other errors, that suggest (at least, to me)
that the parameter is interpreted correctly:

Image Exception : #22 :: ERROR: Could not open image I_brain
Cannot open volume I_brain for reading!
Image Exception : #22 :: ERROR: Could not open image I_brain
Image Exception : #22 :: ERROR: Could not open image I_brain
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
Image Exception : #22 :: ERROR: Could not open image I_grot
Error in slicer input, exiting...
[snip]

However, as soon as I pass any actual value (e.g. -B "-f 0.4"; -B "-f
0.2" etc) I get "Usage: sienax <input> [options] etc etc".

I must be missing something obvious.

Any pointer would be much appreciated.

Thanks,

Lorenzo



[1] http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/SIENA/UserGuide#Usage-1