 |
 |
And once more with the actual attachment (sheesh!) 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 > URL: http://www.fmrib.ox.ac.uk/~flitney > > > > 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 URL: http://www.fmrib.ox.ac.uk/~flitney