hey:
I am not quite sure about what did you guys mean by "not correctly setting the envioronmental variable". When I type "echo $FSLDIR", terminal reponse me with the right path. I strictly followed every step in the online instruction when I was installing FSL. Is that possible that even terminal echoes me the right path, still, my setting of $FSLDIR could be wrong?
Thanks
XC
****************************************
Xuelin Cui
Department of Electrical Engineering
University of Hawaii-Manoa
Honolulu HI 96822
Tel: 1-808-349-0983
Email: [log in to unmask]
****************************************
----- Original Message -----
From: Ged Ridgway <[log in to unmask]>
Date: Tuesday, July 3, 2007 5:37 pm
Subject: Re: [FSL] How to find the exact numeric value of those spatial IC maps in MELODIC?
To: [log in to unmask]
> Hi Xuelin,
>
> Just seen your new post, but I think the error message is clearer
> in
> this one, and almost certainly from the same problem:
>
> > system(['sh -c "FSLOUTPUTTYPE=NIFTI_PAIR; export FSLOUTPUTTYPE;
> $FSLDIR/bin/avwmaths ', fname, ' ', tmpname,'"']);
> [...]
> > "sh; line 1: /bin/avwmaths: No such file or directory"
>
> The error shows that $FSLDIR/bin/avwmaths expanded to just
> /bin/avwmaths, or in other words that $FSLDIR is not set.
>
> You probably need to run something like this first:
> system(['sh -c "source /path/to/your/fsldir/etc/fslconf/fsl.sh"']);
>
> Or maybe just start Matlab after you have set-up FSL in the
> terminal
> window.
>
> Hopefully after that, something like
> system('echo $FSLDIR');
> should show the right location for FSL.
>
> For example, if I run the following lines:
> fslsh = '/my/path/to/fsl/etc/fslconf/fsl.sh';
> cmd = 'avwstats++ $FSLDIR/etc/standard/avg152T1 -x';
> system(['sh -c "source ' fslsh '"']);
> [stat out] = system(['sh -c "' cmd '"'])
>
> I get the result:
> status = 0
> output = 77 76 14
>
> Hope that helps,
> Ged
>
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