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Hi Mark,

Typing <echo $FSLDIR> into a terminal window gives me </usr/local/fsl>

I started matlab by double-clicking on an icon

Thanks for your reply,
Chris


Hi,

What do you get when to do the following in a terminal window:

  echo $FSLDIR

I think the problem might stem from this.

Also, how are you starting matlab?  From the command line, or double-clicking on an icon (or something else)?

All the best,
Mark
On 27 Nov 2013, at 13:41, Maryam Abaei wrote:

> 
> 
> In my case it works for most of the fsl commands, for example randomise in FSLNET, but for some reason it doesn't work for some other commands including slices_summary.
> 
> Best,
> 
> Maryam
> 
> 
> On 27 November 2013 13:32, Niels Bergsland <[log in to unmask]> wrote:
> This shouldn't actually be necessary as long as the /etc/fsl/fsl.sh
> file is sourced. Once sourced, the original fsl command (i.e. those
> without the fsl5.0- prefix) will work as expected.
> 
> 
> 
> On Wed, Nov 27, 2013 at 2:28 PM, Stephen Smith <[log in to unmask]> wrote:
> > Thanks - this is one major thing I really don’t like about the Ubuntu
> > version - they rename all the FSL binaries and scripts so that any other
> > software (eg FSLNets) is not compatible across different operating
> > systems…….hohum!
> >
> > Steve.
> >
> >
> >
> > On 27 Nov 2013, at 07:26, Maryam Abaei <[log in to unmask]> wrote:
> >
> > Hi,
> >
> > I have fsl installed in ubuntu and I had similar error. I had to change
> > "slice_summary" to "fsl5.0-slices_summary" (this is the command I call from
> > a terminal too) in m files, then it worked.
> >
> > Best,
> >
> > Maryam
> >
> >
> > On 27 November 2013 13:14, Stephen Smith <[log in to unmask]> wrote:
> >>
> >> Hi - most likely your call to slices_summary isn’t working right?
> >> Steve.
> >>
> >>
> >>
> >> On 26 Nov 2013, at 09:49, Christophe de Bezenac <[log in to unmask]>
> >> wrote:
> >>
> >> Hi all
> >>
> >> I am trying to run FSLNets by editing nets_examples.m, but when running
> >> <nets_pics(ts,group_maps);> get the following errors:
> >>
> >>
> >> ??? Error using ==> imread at 374
> >> File "grot.png" does not exist.
> >>
> >> Error in ==> nets_pics at 4
> >> picgood=imread('grot.png'); figure; imagesc(picgood);
> >> axis off; title('good components');
> >>
> >>
> >> My group_maps input is
> >> <group_maps='/Users/chdebezenac/fmridata/resting/analysis3.gica/groupmelodic.ica/melodic_IC.nii.gz';>
> >> which I think is correct. Any ideas about what is going wrong?
> >>
> >> Thanks in advance,
> >>
> >> Chris
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> ---------------------------------------------------------------------------
> >> Stephen M. Smith, Professor of Biomedical Engineering
> >> Associate Director,  Oxford University FMRIB Centre
> >>
> >> FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
> >> +44 (0) 1865 222726  (fax 222717)
> >> [log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
> >>
> >> ---------------------------------------------------------------------------
> >>
> >> Stop the cultural destruction of Tibet
> >>
> >>
> >>
> >>
> >
> >
> >
> > ---------------------------------------------------------------------------
> > Stephen M. Smith, Professor of Biomedical Engineering
> > Associate Director,  Oxford University FMRIB Centre
> >
> > FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
> > +44 (0) 1865 222726  (fax 222717)
> > [log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
> > ---------------------------------------------------------------------------
> >
> > Stop the cultural destruction of Tibet
> >
> >
> >
> >
> 
> 
> 
> --
> Niels Bergsland
> Integration Director
> Buffalo Neuroimaging Analysis Center
> 100 High St. Buffalo NY 14203
> [log in to unmask]
> (716) 859-7677
>