Hi,
OK, the bash script will be complicated.
However, calling it from the command line should work fine.
Can you give me the exact command you are running and the
exact error output?
All the best,
Mark
On 10 Jan 2011, at 17:14, Graeme Schwindt wrote:
> Hi Mark,
>
> Thanks for your reply. This is simply running from the command line, or calling it from within a bash script, so it seems there is something going on. We're running fsl 4.1
>
> On Mon, Jan 10, 2011 at 12:08 PM, Mark Jenkinson <[log in to unmask]> wrote:
> Hi,
>
> Are you doing this from within a script or trying to run it on a cluster?
> That can make it difficult with the quotes.
>
> If you are using fsl_sub to run it on a cluster then I recommend
> using the -t option and putting the command, with quotes as usual,
> into the file that is specified by -t. This will run it correctly on the
> cluster.
>
> If you are doing it within your own script then it is trickier, but
> running it with the fsl_sub and -t is still an option, although
> you will need to make any subsequent commands that depend
> on the output run with another fsl_sub job that has a hold on
> the first job number.
>
> If you are running this directly on the command line and still
> having trouble then please let us know, as that would indicate
> more fundamental problems.
>
> All the best,
> Mark
>
>
>
> On 10 Jan 2011, at 15:49, Graeme Schwindt wrote:
>
> > I'm having some odd trouble with getting sienax to run with -B options
> >
> > Command is: sienax patient_T1.img -B "-f 0.2"
> >
> > But simply returns the usage, indicating some kind of error in the command - anyone have any clue what's going on? It will run fine with "-R" in quotes, but trying to change f is not working....
> >
> > Thanks
> >
> > Graeme
>
>
>
> --
> Graeme C. Schwindt, HBSc
> MD/PhD Student
> University of Toronto
> [log in to unmask]
>
|