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...
closing volume...
{??? Undefined function or method 'fspecial' for input arguments of type
'char'.
Error in ==> make_outer_surface at 31
Gaussian = fspecial('gaussian',[2 2],1);
}
>>
ERROR: make_outer_surface did not create output file
'/data/Projekte/Freesurfer/Prob1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!
Linux beo-08 2.6.32.59-ql-beowulf-37 #1 SMP Sat Mar 31 14:31:51 CEST 2012
x86_64 GNU/Linux
recon-all -s Prob1 exited with ERRORS at Tue Nov 19 08:02:22 CET 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
---------------
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
On Nov 18, 2013, at 11:26 PM, "Jockwitz, Christiane"
<c.jockw...@fz-juelich.de<mailto:c.jockw...@fz-juelich.de>> wrote:
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.sch...@unige.ch<http://unige.ch>]
Gesendet: Montag, 18. November 2013 21:03
An: Jockwitz, Christiane
Cc: freesurfer@nmr.mgh.harvard.edu<mailto: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.jockw...@fz-juelich.de<mailto:c.jockw...@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>
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