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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 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 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 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 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 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.es http://www.upo.es/neuroaging/es/
freesurfer@nmr.mgh.harvard.edu
-
Gabriel Gonzalez Escamilla -
Marie Schaer