Dear Sebastian,
Im still working on my problem. I tried to put a symbolic link to the matlab
binary and got the following answer:
bash-3.2$ ln -s /Users/dhirjak/MATLAB_R2013a.app/bin/matlab
/Users/dhirjak/bin/matlab
ln: /Users/dhirjak/bin/matlab: No such file or directory
bash-3.2$ ln -s /Users/dhirjak/MATLAB_R2013a.app/bin/matlab
/Users/dhirjak/freesurfer/matlab
ln: /Users/dhirjak/freesurfer/matlab/matlab: Permission denied
bash-3.2$
I also tried to add path in matlab, but it is still not working.
What is the problem??? What does it mean "permission denied"??? What should I
do next?
Many thanks,
DH
> From: sebastian.moell...@rwth-aachen.de
> Date: Sun, 26 Jan 2014 16:33:40 +0100
> To: gr...@nmr.mgh.harvard.edu
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Freesurfer, Matlab and Maverick
>
> Hi Dusan,
>
>
> On Jan 26, 2014, at 15:36 , Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote:
>
> >
> > Hi Dusan, find out where matlab is and add it to your path. Eg, on my mac
> > matlab is here
> >
> > /Applications/MATLAB_R2011b.app/bin/matlab
> >
> > In my .cshrc file, I have
> > set path = ($path /Applications/MATLAB_R2011b.app/bin/matlab)
>
> Should you use bash, add the following two lines to your .bashrc:
>
> PATH= /Applications/MATLAB_R2011b.app/bin/matlab:$PATH
> export PATH
>
> Or you can put a symbolic link to the matlab binary to a directory that is
> already in your path:
> "ln -s /Applications/MATLAB_R2011a.app/bin/matlab /usr/local/bin/matlab"
> (the first is more comprehensive and will also allow mex from the terminal,
> but I do not think that you really care for that too much...)
>
>
>
> (In case you wonder what shell you use, type "echo $0" in a terminal:
> hms-beagle:~ moeller$ echo $0
> -bash
> hms-beagle:~ moeller$ tcsh
> [hms-beagle:~] moeller% echo $0
> tcsh
> [hms-beagle:~] moeller%
>
> e.g. I run bash by default, but after starting tcsh it reports tcsh; for bash
> edit ~/.bashrc, for tcsh edit ~/.cshrc. I think that the nano editor is part
> of macosx, so "nano ~/.bashrc" or "nano ~/.cshrc" should work, edit the file
> then use control-x to exit nano, it will ask whether you want to save…)
>
> best
> Sebastian
>
> >
> > doug
> >
> >
> >
> > On 1/26/14 9:28 AM, Dusan Hirjak wrote:
> >> Hi Sebastian,
> >>
> >> I typed "matlab" and "getmatlab" in my terminal, but it did not work. When
> >> I typed getmatlab in my terminal I got the following message: "ERROR:
> >> Cannot find matlab. Does not exist or is not in path."
> >>
> >> Typing "matlab" is not working either:-( "command not found" is the answer.
> >>
> >> I guess your hypothesis is true and the matlab binary is not in my path.
> >> Why not? What should I do next?
> >>
> >> Thanks a lot!
> >>
> >> DH
> >>
> >>
> >> > Subject: Re: [Freesurfer] Freesurfer, Matlab and Maverick
> >> > From: sebastian.moell...@rwth-aachen.de
> >> > Date: Sun, 26 Jan 2014 10:33:33 +0100
> >> > CC: freesurfer@nmr.mgh.harvard.edu
> >> > To: dusanhir...@hotmail.com
> >> >
> >> > Hi Dusan,
> >> >
> >> > (I saw your PN earlier but had no idea and hence did not reply).
> >> > But this has more information, so I try again ;)
> >> >
> >> >
> >> > On Jan 25, 2014, at 02:00 , Dusan Hirjak <dusanhir...@hotmail.com> wrote:
> >> >
> >> > > Dear Freesurferexperts,
> >> > >
> >> > > I still have the Problem because I can not run the the mris-command to
> >> > > estimate the gyrification-index, because Freesurfer is not recognizing
> >> > > Matlab: "ERROR: Matlab is required to run mris_compute_lgi"
> >> > > Im not sure why this is happening? Does someone have an idea???
> >> >
> >> > Could you, please open a terminal and type: 'matlab'. It should open a
> >> > matlab window, but I suspect that it does not work on your system. My
> >> > hypothesis is that either the binary/script to start matlab is not
> >> > called matlab (unlikely) or that the directory with the matlab binary is
> >> > not in your path and hence LGI can not start matlab.
> >> > Anyway, if calling "matlab" from the terminal works my hypothesis is
> >> > falsified, but give it a try, please.
> >> >
> >> > best regards
> >> > Sebastian
> >> >
> >> >
> >> >
> >> > >
> >> > > Im starting Freesurfer as follows:
> >> > >
> >> > > FREESURFER_HOME=/Users/dhirjak/freesurfer
> >> > >
> >> > > source $FREESURFER_HOME/SetUpFreeSurfer.sh
> >> > >
> >> > > (than I get the following output)
> >> > >
> >> > > Dusan-Hirjaks-MacBook-Pro:~ dhirjak$ source
> >> > > $FREESURFER_HOME/SetUpFreeSurfer.sh
> >> > > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------
> >> > > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> >> > > FREESURFER_HOME /Users/dhirjak/freesurfer
> >> > > FSFAST_HOME /Users/dhirjak/freesurfer/fsfast
> >> > > FSF_OUTPUT_FORMAT nii.gz
> >> > > SUBJECTS_DIR /Users/dhirjak/MRI/Freesurfer_2
> >> > > MNI_DIR /Users/dhirjak/freesurfer/mni
> >> > > FSL_DIR /Users/dhirjak/fsl
> >> > >
> >> > > export SUBJECTS_DIR=/Users/dhirjak/MRI/Freesurfer
> >> > >
> >> > >
> >> > > In have the following lines in my matlab startup-file:
> >> > >
> >> > > fshome = getenv('FREESURFER_HOME');
> >> > > fsmatlab = sprintf('%s/matlab',fshome);
> >> > > if (exist(fsmatlab) == 7)
> >> > > path(path,fsmatlab);
> >> > > end
> >> > > clear fshome fsmatlab;
> >> > > fsfasthome = getenv('FSFAST_HOME');
> >> > > fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
> >> > > if (exist(fsfasttoolbox) == 7)
> >> > > path(path,fsfasttoolbox);
> >> > > end
> >> > > clear fsfasthome fsfasttoolbox;
> >> > >
> >> > > Thanks!!!
> >> > >
> >> > > Dusan Hirjak
> >> > >
> >> > >
> >> > >
> >> > >
> >> > >
> >> > >
> >> > > _______________________________________________
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> >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> > >
> >> > >
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> >>
> >>
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