[Freesurfer] error measuring LGI
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 matchSubject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0INFO: SUBJECTS_DIR is /root/trabajo/freesurfer/subjectsActual 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.logLinux 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.pialERROR: 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/Linuxrecon-all -s c_Macarena exited with ERRORS at Tue Oct 16 15:24:31 CEST 2012Matlab 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
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Re: [Freesurfer] error measuring LGI
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 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
>
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>
>
> 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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Re: [Freesurfer] error measuring LGI
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,GabrielEl 16/10/12, Marie Schaer 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,MarieOn 16 oct. 2012, at 16:02, Gabriel Gonzalez Escamilla 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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/
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Re: [Freesurfer] error measuring LGI
Dear Marie,I've tried to set the matlab installation path, into the tcsh path (where my FS_HOME is), but It's not working. I have no idea how to change this on the startup.m, can you help me with it?Regards,GabrielEl 16/10/12, Marie Schaer 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,MarieOn 16 oct. 2012, at 16:02, Gabriel Gonzalez Escamilla 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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/
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Re: [Freesurfer] error measuring LGI
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 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 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 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: ggon...@upo.es
> http://www.upo.es/neuroaging/es/
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Re: [Freesurfer] error measuring LGI
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 stillAny ideas?GabrielEl 16/10/12, Marie Schaer 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.MarieOn 16 oct. 2012, at 16:39, Gabriel Gonzalez Escamilla > 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,GabrielEl 16/10/12, Marie Schaer > 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,MarieOn 16 oct. 2012, at 16:02, Gabriel Gonzalez Escamilla > 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 listFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.es http://www.upo.es/neuroaging/es/
-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] error measuring LGI
... 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 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 > > 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 >
>>> 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 >>> > 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
Re: [Freesurfer] error measuring LGI
Thank you Marie!Option 2 works, when I did erase the variables and set them again finally worked!!!You are so helpful!!!GabrielEl 16/10/12, Marie Schaer escribió:... 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,MarieOn 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 stillAny ideas?GabrielEl 16/10/12, Marie Schaer > 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.MarieOn 16 oct. 2012, at 16:39, Gabriel Gonzalez Escamilla >> 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,GabrielEl 16/10/12, Marie Schaer >> 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,MarieOn 16 oct. 2012, at 16:02, Gabriel Gonzalez Escamilla >> 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 listFreesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: >ggon...@upo.es >http://www.upo.es/neuroaging/es/
-- --PhD. student Gabriel González-EscamillaLaboratory of Functiona
