... 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.Schaer@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 <ggonesc@upo.es ggonesc@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.Schaer@unige.ch Marie.Schaer@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 <ggonesc@upo.es ggonesc@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.eduFreesurfer@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 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
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: ggonesc@upo.esggonesc@upo.es ggonesc@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: ggonesc@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.