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
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