... Strange, then I would just quickly look at the following things (in a new
terminal, so that you are sure that everything is cleanly set):
1) whether the $PATH is indeed correctly set without typo. Either by verifying
the $PATH variable (type $PATH in your shell, you should see your full path to
matlab). Or by just prompting the command matlab in your shell, which should
open a matlab session.
2) I would source the freesurfer environment variables again (set the
FREESURFER_HOME variable and then source SetUpFreeSurfer.csh), and check
whether getmatlab give you the location of your matlab command (something like
/root/trabajo/matlab2009/bin/matlab)
Given that I am not a centOS specialist, if this doesn't work, we should maybe
ask someone else, like e.g. Nick if he has a better idea.
Let me know,
Marie
On Oct 16, 2012, at 6:54 PM, Gabriel Gonzalez Escamilla wrote:
> Marie,
>
> I'm working on centOS 4, I'd add the path to the matlab installation folder
> on my PATH as:
> setenv MATLABPATH /root/trabajo/matlab2009
> setenv PATH ${MATLABPATH}/bin:${PATH}
>
> And this is not working still
> Any ideas?
>
> Gabriel
>
>
> El 16/10/12, Marie Schaer <marie.sch...@unige.ch> escribió:
>>
>>
>>
>> Gabriel,
>>
>> I would start by adding the path to the matlab installation directory to
>> $PATH. On a Mac it looks like /Applications/Matlab_R*/bin. Then the
>> getmatlab command should work, and LGI as well.
>>
>> Marie
>>
>> On 16 oct. 2012, at 16:39, Gabriel Gonzalez Escamilla <ggon...@upo.es
>> <ggon...@upo.es>> wrote:
>>
>>
>>> Thanks Marie,
>>>
>>> You are right is pointing to the FSmatlab directory not to the installation
>>> folder, but the wiki say so:
>>>
>>> "You will also need $FREESURFER_HOME/matlab in your matlab path set up in
>>> your ~/matlab/starup.m script. "
>>>
>>> Do I need to change that in the startup.m?
>>> I did also try the getmatlab command and said that matlab does not exist,
>>> I'm guessing this is the problem.
>>>
>>> Bests,
>>> Gabriel
>>>
>>>
>>> El 16/10/12, Marie Schaer <marie.sch...@unige.ch <marie.sch...@unige.ch>>
>>> escribió:
>>>>
>>>> Gabriel,
>>>>
>>>> If I am correct, your path (fsmatlab) is pointing to the matlab folder of
>>>> freesurfer distribution (I.e. Including the matlab scripts) whereas it
>>>> should point to the matlab installation directory.
>>>>
>>>> You can check using the command getmatlab.
>>>>
>>>> Let me know,
>>>>
>>>> Marie
>>>>
>>>> On 16 oct. 2012, at 16:02, Gabriel Gonzalez Escamilla <ggon...@upo.es
>>>> <ggon...@upo.es>> wrote:
>>>>
>>>> > Dear FS experts
>>>> >
>>>> > I'm trying to run the "recon-all -s subjid -localGI" in both terminal
>>>> > and matlab, and neither of them is working.
>>>> > I'm using currently version of FS and matlab R2009b.
>>>> >
>>>> > the following error alwais apair:
>>>> >
>>>> > INFO: FreeSurfer build stamps do not match
>>>> > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0
>>>> > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
>>>> > INFO: SUBJECTS_DIR is /root/trabajo/freesurfer/subjects
>>>> > Actual FREESURFER_HOME /root/trabajo/freesurfer
>>>> > -rwxr-xr-x 1 root root 6867734 Oct 16 15:23
>>>> > /root/trabajo/freesurfer/subjects/c_Macarena/scripts/recon-all.log
>>>> > Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT
>>>> > 2006 x86_64 x86_64 x86_64 GNU/Linux
>>>> > /root/trabajo/freesurfer/subjects/c_Macarena/surf
>>>> > #--------------------------------------------
>>>> > #@# Local Gyrification Index lh Tue Oct 16 15:24:31 CEST 2012
>>>> >
>>>> > mris_compute_lgi --i lh.pial
>>>> >
>>>> > ERROR: Matlab is required to run mris_compute_lgi!
>>>> > Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT
>>>> > 2006 x86_64 x86_64 x86_64 GNU/Linux
>>>> >
>>>> > recon-all -s c_Macarena exited with ERRORS at Tue Oct 16 15:24:31 CEST
>>>> > 2012
>>>> >
>>>> >
>>>> >
>>>> >
>>>> > Matlab exist on the startup.m file as:
>>>> >
>>>> > %------------ FreeSurfer -----------------------------%
>>>> > fshome = getenv('FREESURFER_HOME');
>>>> > fsmatlab = sprintf('%s/root/trabajo/freesurfer/matlab',fshome);
>>>> > path(path,fsmatlab);
>>>> > clear fshome fsmatlab;
>>>> > %-----------------------------------------------------%
>>>> >
>>>> >
>>>> > Can anyone help me on this?
>>>> >
>>>> > Best Regards,
>>>> > Gabriel
>>>> >
>>>> > _______________________________________________
>>>> > Freesurfer mailing list
>>>> > <Freesurfer@nmr.mgh.harvard.edu>Freesurfer@nmr.mgh.harvard.edu
>>>> > <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
>>>> > e-mail
>>>> > contains patient information, please contact the Partners Compliance
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>>>> > but does not contain patient information, please contact the sender and
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>>>
>>> --
>>> --------------------------
>>> PhD. student Gabriel González-Escamilla
>>> Laboratory of Functional Neuroscience
>>> Department of Physiology, Anatomy, and Cell Biology
>>> University Pablo de Olavide
>>> Ctra. de Utrera, Km.1
>>> 41013 - Seville
>>> - Spain -
>>>
>>> Email: <ggon...@upo.es>ggon...@upo.es <ggon...@upo.es>
>>> http://www.upo.es/neuroaging/es/
>
> --
> --------------------------
> PhD. student Gabriel González-Escamilla
> Laboratory of Functional Neuroscience
> Department of Physiology, Anatomy, and Cell Biology
> University Pablo de Olavide
> Ctra. de Utrera, Km.1
> 41013 - Seville
> - Spain -
>
> Email: ggon...@upo.es
> http://www.upo.es/neuroaging/es/
> _______________________________________________
> 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 e-mail
> contains patient information, please contact the Partners Compliance HelpLine
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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