Oh. Looks like you guys have discovered more issues with /bin/sh on your machine than I needed to fix on ours. 

Michela, could you send us diffs for your modified scripts and I'll see to it that subsequent version have the most compatible subset of shell commands. NB. Use diff -Naur <original> <modified> to make patchable diffs.
 
On 24 Apr 2008, at 09:39, Dave Flitney wrote:

And once more with the actual attachment (sheesh!)

<bedpostx.patch>


Okay, checking on a Solaris machine /bin/sh is a bit different and test -z doesn't work consistently. Grrr!

Try the applying the attached patch: save it into a file, ~/bedpostx.patch, then cd into $FSLDIR/bin and run:

flitney$ patch < ~/bedpostx.patch

On 23 Apr 2008, at 11:04, Dave Flitney wrote:

Sorry for not getting back to you sooner. Just in case it's still relevant...

On 11 Apr 2008, at 16:48, Michela Pievani wrote:

Specifically, the error with fdt reported by LOG file is this:

cat LOG

cp -r /home/local/FSL4/feeds/data/fdt_subj1 /home/local/FSL4/feeds/results

unset FSLMACHINELIST; /home/local/FSL4/fsl/bin/bedpostx /home/local/FSL4/feeds/results/fdt_subj1 -n 1
subjectdir is /home/local/FSL4/feeds/results/fdt_subj1
/home/local/FSL4/fsl/bin/bedpostx: test: argument expected

To check what's wrong with this, I am running bedpostx checking the output by step the output.
It came out that the syntax is the problem, in that the script uses /bin/sh but ny $SHELL is csh. Don't know whether should I change this. When I installed fsl I set "SHELL = /bin/sh" (default value) in systemvars.mk.

The scripts specify the desired shell directly so you don't need to change shells to run our scripts. If you want to step through our script commands by copying them to the command line then this would be a problem and you'd need to invoke a /bin/sh compatible shell such as sh or bash first. 

I'm a little surprised you're having these difficulties though since these scripts are so heavily used both in-house and externally. I'm not aware that solaris /bin/sh is particularly different from others but... Also fdt is the last of the tests and I am surprise the others previous steps didn't fail. Could you send me your full LOG file?

Cheers, Dave

--
Dave Flitney, IT Manager
Oxford Centre for Functional MRI of the Brain
E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717





Cheers, Dave

--
Dave Flitney, IT Manager
Oxford Centre for Functional MRI of the Brain
E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717





Cheers, Dave

--
Dave Flitney, IT Manager
Oxford Centre for Functional MRI of the Brain
E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717