Hi Jon,
I guess you don't have the image processing toolbox installed with matlab? fspecial is a matlab function comprised in this toolbox… I am afraid that lGI with not run without it.
Marie
On Mar 18, 2013, at 12:03 PM, Jon Wieser wieser@uwm.edu wrote:
I added the matlab bin directory to my PATH.
getmatlab /Applications/MATLAB_R2012b.app/bin/matlab
I ran : recon-all -s freesurfer -localGI and got the following:
Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0001 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-rw- 1 wieser admin 450426 Mar 18 13:58 /Studies/MJMRI/MJ0001/freesurfer/scripts/recon-all.log Darwin psy-cerebellum.wifi.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 /Studies/MJMRI/MJ0001/freesurfer/surf #-------------------------------------------- #@# Local Gyrification Index lh Mon Mar 18 13:59:36 CDT 2013 \n mris_compute_lgi --i lh.pial \n ================= rm -Rf /Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit =================
< M A T L A B (R) > Copyright 1984-2012 The MathWorks, Inc. R2012b (8.0.0.783) 64-bit (maci64) August 22, 2012To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com.
reading filled volume...
closing volume... Undefined function 'fspecial' for input arguments of type 'char'.
Error in make_outer_surface (line 31) Gaussian = fspecial('gaussian',[2 2],1);
ERROR: make_outer_surface did not create output file '/Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Darwin psy-cerebellum.wifi.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
recon-all -s freesurfer exited with ERRORS at Mon Mar 18 13:59:49 CDT 2013
For more details, see the log file /Studies/MJMRI/MJ0001/freesurfer/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
----- Original Message ----- From: "Marie Schaer" Marie.Schaer@unige.ch To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Monday, March 18, 2013 1:07:54 PM Subject: Re: [Freesurfer] LGI
Hi Jon,
It looks like the matlab path is not set on your machine. Can you set the $PATH environment variable to include the path to the matlab functions as well? You can try to launch the command "getmatlab", if you get the answer that matlab is not installed, it means that the $PATH environment variable is not properly set. You can also look on the mailing list, there are a few explanations about this path issue, among which the following one: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25017.html
Let me know if you don't find how to make it work.
Best,
Marie
On Mar 18, 2013, at 10:44 AM, Jon Wieser < wieser@uwm.edu > wrote:
i am trying to computer the LGI local gyrification index with freesurfer. I have Matlab on my machine. I got the following error:
recon-all -s freesurfer -localGI Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 wieser admin 506264 Mar 18 12:37 /Studies/MJMRI/MJ0012/freesurfer/scripts/recon-all.log Darwin psy-cerebellum.wifi.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 /Studies/MJMRI/MJ0012/freesurfer/surf #-------------------------------------------- #@# Local Gyrification Index lh Mon Mar 18 12:43:04 CDT 2013 \n mris_compute_lgi --i lh.pial \n ERROR: Matlab is required to run mris_compute_lgi! Darwin psy-cerebellum.wifi.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
recon-all -s freesurfer exited with ERRORS at Mon Mar 18 12:43:04 CDT 2013
For more details, see the log file /Studies/MJMRI/MJ0012/freesurfer/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
JOn
-- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219