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
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