Albert,

It appears to be failing when the mris_compute_lgi script first attempts a call to matlab. To debug, try this:

cd $SUBJECTS_DIR/dinghai_4/surf mris_compute_lgi --i lh.pial --debug

and follow the output to trace where it is failing. notice that mris_compute_lgi creates a temporary .m file off the /tmp directory, which is then called by matlab. So you will need to figure out where in that sequence it is failing. It calls matlab from the script by 'catting' and piping the file through matlab, ie, something like this:

cat /tmp/mos_26429_.m | /usr/local/bin/matlab -display iconic -nojvm -nosplash

Nick

On Tue, 2009-08-25 at 10:21 +0800, leemon albert wrote:

Dear all,

I am trying to compute the local gyrification index but unfortunately encounter the problem below. Matlab Version ( R2007a) and also the Image Processing Toolbox are installed on my computer (Ubuntu 9.04,32-bit).

I think the matlab isn't rightly called by the script. But the "make_outer_surface.m" is not a bash command. Here, how does it invoke the Matlab?

Any help is greatly appreciated!

Best wishes,

/mnt/freesurfer/subjects$ recon-all -s dinghai_4 -localGI Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /mnt/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 huiguang huiguang 803627 Aug 25 09:44 /mnt/freesurfer/subjects/dinghai_4/scripts/recon-all.log Linux hhg-linux 2.6.24-19-generic #1 SMP Wed Aug 20 22:56:21 UTC 2008 i686 GNU/Linux /mnt/freesurfer/subjects/dinghai_4/surf #-------------------------------------------- #@# Local Gyrification Index lh Tue Aug 25 09:54:08 CST 2009

mris_compute_lgi --i lh.pial

================= rm

-Rf /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial

================= mkdir

-p /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial

================= mris_fill -c -r 1 lh.pial /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /mnt/freesurfer/subjects/dinghai_4/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('/mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= if: Expression Syntax.

ERROR: make_outer_surface did not create output file '/mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux hhg-linux 2.6.24-19-generic #1 SMP Wed Aug 20 22:56:21 UTC 2008 i686 GNU/Linux

recon-all exited with ERRORS at Tue Aug 25 09:54:18 CST 2009

Then I open the matlab ,there is a warning: "Executing startup failed in matlabrc.',... 'This indicates a potentially serious problem in your MATLAB setup,',... 'which should be resolved as soon as possible. "

-- Albert Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA

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