Dear Doug

Thanks again for your help. I think I have added the path to my linux path. This is what I have done:

Andres-MacBook-Pro:~ andre$ echo $PATH

/Applications/fsl/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin

Andres-MacBook-Pro:~ andre$ PATH=/Applications/fsl/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/matlab/MATLAB_R2014a.app/bin/matlab

Andres-MacBook-Pro:~ andre$ export FREESURFER_HOME=/Applications/freesurfer

Andres-MacBook-Pro:~ andre$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

-------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME /Applications/freesurfer

FSFAST_HOME /Applications/freesurfer/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR /Applications/freesurfer/subjects

MNI_DIR /Applications/freesurfer/mni

FSL_DIR /Applications/fsl/fsl

Andres-MacBook-Pro:~ andre$ cd /Applications/freesurfer/subjects

Andres-MacBook-Pro:subjects andre$ recon-all -s subj001 -localGI

Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects

Actual FREESURFER_HOME /Applications/freesurfer

-rw-rw-r-- 1 andre staff 130383 Dec 14 11:44 /Applications/freesurfer/subjects/subj001/scripts/recon-all.log

Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64

/Applications/freesurfer/subjects/subj001/surf

#--------------------------------------------

#@# Local Gyrification Index lh Wed Dec 14 13:15:53 GMT 2016

\n mris_compute_lgi --i lh.pial \n

ERROR: Matlab is required to run mris_compute_lgi!

Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64

recon-all -s subj001 exited with ERRORS at Wed Dec 14 13:15:53 GMT 2016

For more details, see the log file /Applications/freesurfer/subjects/subj001/scripts/recon-all.log

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

I am still receiving the same error message. Do you have another clue what is going wrong here?

Best wishes

André

Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edu]
Gesendet: Dienstag, 13. Dezember 2016 22:53
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] recon-all -s <subj> -localGI

Is matlab in your linux path? On my mac, I had to add this path to my linux path: /Applications/MATLAB_R2011b.app/bin/matlab

On 12/13/16 11:16 AM, André Schmidt wrote:

Many thanks for your help. According to your suggestion, I modified the start.up file in Users/andre/matlab/startup.m (see attached).

However, I got the following error:
Andres-MacBook-Pro:~ andre$ export FREESURFER_HOME=/Applications/freesurfer

Andres-MacBook-Pro:~ andre$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

-------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME /Applications/freesurfer

FSFAST_HOME /Applications/freesurfer/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR /Applications/freesurfer/subjects

MNI_DIR /Applications/freesurfer/mni

FSL_DIR /Applications/fsl/fsl

Andres-MacBook-Pro:~ andre$ cd /Applications/freesurfer/subjects

Andres-MacBook-Pro:subjects andre$ recon-all -s subj001 -localGI

Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects

Actual FREESURFER_HOME /Applications/freesurfer

-rw-rw-r-- 1 andre staff 81473 Dec 13 17:09 /Applications/freesurfer/subjects/subj001/scripts/recon-all.log

Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64

/Applications/freesurfer/subjects/subj001/surf

#--------------------------------------------

#@# Local Gyrification Index lh Tue Dec 13 17:22:19 GMT 2016

\n mris_compute_lgi --i lh.pial \n

ERROR: Matlab is required to run mris_compute_lgi!

Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64

recon-all -s subj001 exited with ERRORS at Tue Dec 13 17:22:19 GMT 2016

For more details, see the log file /Applications/freesurfer/subjects/subj001/scripts/recon-all.log

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Do you know why it's still not working?

Thanks again and best wishes

André
Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edu]
Gesendet: Dienstag, 13. Dezember 2016 16:26
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] recon-all -s <subj> -localGI
The LGI routines run matlab (even though you never actually run any matlab commands yourself). But you have to make sure that matlab knows where the LGI matlab routines are. To do this you must modify your matlab ~/matlab/startup.m file to add the path to the LGI routines to your path. To do this, add the following lines to your startup.m

FSH = getenv('FREESURFER_HOME');

fshmatlab = sprintf('%s/matlab',FSH);
path(path,fshmatlab);
clear fshmatlab FSH;

On 12/13/16 10:10 AM, André Schmidt wrote:
Dear experts

I am trying to compute the local gyrification index but I am not sure how I have to do the following:

"You will also need $FREESURFER_HOME/matlab in your matlab path set up in your ~/matlab/starup.m script."

Can you please quickly help me what I need to type in the terminal to do this in order to run recon-all -s <subj> -localGI?

Many thanks for your help!

Best wishes

André
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