Hi,
First of all, you are using the old wiki documentation (for FSL versions 4.x).
Second, the advice on this page says to do this "assuming FSL is installed in /usr/local" which in your case it is not. So what you've done to fix this is what the documentation actually suggests and so this is definitely the correct thing to do.
All the best,
Mark
On 19 Jul 2014, at 20:55, charlie <[log in to unmask]> wrote:
> I attempted to load some FSL .nii.gz files into matlab but the path was not recognized. Initially I tried making a startup.m file using the syntax
>
> setenv( 'FSLDIR', '/usr/local/fsl');
> fsldir = getenv('FSLDIR');
> fsldirmpath = sprintf('%s/etc/matlab',fsldir);
> path(path, fsldirmpath);
> clear fsldir fsldirmpath;
>
> from
>
> http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fsl/macosx.html#matlab
>
> but this resulted in this error in matlab
>
> Warning: Name is nonexistent or not a
> directory: /usr/local/fsl/etc/matlab.
>> In path at 110
> In startup at 4
>
> I then check the dir /usr/local/fsl/etc/matlab
> but fsl did not have a path in this location, but rather in applications/fsl/etc/matlab
>
> setenv( 'FSLDIR', '/Applications/fsl');
> fsldir = getenv('FSLDIR');
> fsldirmpath = sprintf('%s/etc/matlab',fsldir);
> path(path, fsldirmpath);
> clear fsldir fsldirmpath;
>
> this now works, in so far as I can use the read_avw function but this may not be an optimal solution.
>
> Any recommendations would be much appreciated. I have had zero problems with FSL...
>
> The version of matlab I'm using is 7.14 R2012a; the version of FSL is 5.0.1, FLIRT version 6.0, echo $FSLDIR returns the expected /Applications/fsl
>
> All the best
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