Finally, I was able to add the path: export PATH=$PATH:/Applications/matlab/MATLAB_R2014a.app/bin/ Unfortunately, I receive a new error:
ERROR: make_roi_paths did not complete successfully!
Do you know what happened now? To compute LGI, I just use the rh.pial and lh.pial from recon-all <subjid> all (only these two files are in the surf directory). Do I need all files from recon-all <subjid> all?
Many thanks for your help again André
________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 14. Dezember 2016 17:03 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] recon-all -s <subj> -localGI
What happens if you run getmatlab ?
On 12/14/16 7:14 AM, André Schmidt wrote: Dear Doug
Thanks again for your help. I think I have added the path to my linux path. This is what I have done:
Andres-MacBook-Pro:~ andre$ 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.h...
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu] Gesendet: Dienstag, 13. Dezember 2016 22:53 An: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu] Gesendet: Dienstag, 13. Dezember 2016 16:26 An: freesurfer@nmr.mgh.harvard.edumailto: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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