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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [gr...@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
startup.m
Description: startup.m
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