André, It looks like you have the matlab path typed correctly. I would try to tab complete it in a terminal to check. You currently have it typed as this: /Applications/matlab/MATLAB_R2014a.app/bin/matlab I expect it to be this on your computer: /Applications/MATLAB_R2014a.app/bin/matlab
Try doing it through tab complete. then hit enter, if matlab opens that is the correct path to add. hth d On Wed, Dec 14, 2016 at 11:13 AM, André Schmidt <andre.schm...@unibas.ch> wrote: > I get the following: > > Andres-MacBook-Pro:subjects andre$ getmatlab > ERROR: Cannot find matlab. > Does not exist or is not in path. > > I guess adding the path (or what I defined as path) didn't work. > > Bw > 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: Mittwoch, 14. Dezember 2016 17:03 > > An: freesurfer@nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] recon-all -s <subj> -localGI > > What happens if you run getmatlab ? > > > On 12/14/16 7:14 AM, André Schmidt wrote: > > 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-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 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-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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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
