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
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > _______________________________________________
>> > > Freesurfer mailing list
>> > > Freesurfer@nmr.mgh.harvard.edu
>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> > >
>> > >
>> > > The information in this e-mail is intended only for the person to whom
>> > > it is
>> > > addressed. If you believe this e-mail was sent to you in error and the
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>> > > contains patient information, please contact the Partners Compliance
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>> > > properly
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>> >
>>
>>
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>>
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