Christiane, 

The log you sent me doesn't correspond to the error you first wrote in your email. The error reads as follow in your log:

---------------

>> reading filled volume...

---------------

It doesn't find the fspecial.m function, probably because you don't have the licence for the image processing toolbox in your installation. Is there a way you can add the toolbox to your matlab installation?

Marie

NB: no need to change the matlab path, it's already correctly set up

Hi Marie,

 

with the old path I ment that the path just did not change. Here is my entire log.

 

Thank you very much for your help.

 

Kind regards

Christiane

 

Von: Marie Schaer [mailto:Marie.Schaer@unige.ch] 
Gesendet: Montag, 18. November 2013 21:03
An: Jockwitz, Christiane
Cc: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] localGI Matlabpath

 

 

 

Hi Christiane,

 

What do you mean when you say that you get the old path with getmatlab?

 

In any case, the error seems not related to a matlab path issue. Can you please attach the entire log?

 

Marie

 

On Nov 18, 2013, at 12:03 AM, "Jockwitz, Christiane" <c.jockwitz@fz-juelich.de>

 wrote:

Dear Freesurfer experts,

 

I tried to run the local GI command recon-all –s –localGI and got the following error message:

 

>> ??? Undefined function or method 'make_outer_surface' for input arguments of

type 'char'.

 

From earlier post I tried to fix the problem by changing the matlabpath like this:

 

setenv MATLABPATH /directory/bin

> setenv PATH ${MATLABPATH}/bin:${PATH}

 

However, if I then check the path via „getmatlab“ I still get the old path. Did I do something wrong?

And is it right to set up my matlabpath to the matlab/bin folder?

 

The scripts like make_outer_surface.m are located in the freesurfer/matlab directory. Or does the path have to point to the scripts directly?

 

Thank you very much in advance

 

Kind regards,

Christiane

 

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<recon-all.log>