Many thanks for the immediate response.
I changed the two lines in the bin/siena directory but the same error occured again. I then changed the two lines in the stable-src directory as well and tried it vice versa but it didn't work. I had a look at the rest of the code and thought maybe I need to add some lines to section for opts. Something like: if $opts = -g then betf= whatever. As I said I have not very much knowledege about programing or so :-)
thanks again
Alex
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Von: FSL - FMRIB's Software Library im Auftrag von Stephen Smith
Gesendet: Mi 30.07.2003 14:06
An: [log in to unmask]
Betreff: Re: [FSL] BET, SIENA, parameters
Hi - that makes sense. SIENA doesn't allow you to put all possible bet
options into the command line, only the -f one.
To get more fine control of bet inside the SIENA script, take a local copy
of fsl/bin/siena and edit the 2 bet lines that start with
${FSLDIR}/bin/bet
adding in any other options before the ">>"
Thanks, Steve.
On Wed, 30 Jul 2003, Alex Mohr wrote:
> Hello,
>
>
> The BET leaves a lot of orbital and petroclival tissue in our data so i
> modified the fractional intensity and threshold gradient values until
> results were acceptable. But when trying to use these values in SIENA the
> programm fails. I just added "-f 0.6 -g - 0.2" in the command line. The
> errors are: dc: stack empty, Canīt open file1_to_file2_flow.hdr, cannot
> open volume file1_halfwayto_file2.hdr for reading. Any other help regarding
> the aspect of removing orbital and petroclival tissue would be appreciated
> as well. I am completely new to FSL so probably there are some otehr tricks.
>
> Many thanks in advance
>
> Alex Mohr
>
Stephen M. Smith MA DPhil CEng MIEE
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe 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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