Dear all,
<br>
<br>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). <br>
<br>I think the matlab isn&#39;t rightly called by  the script. But the &quot;make_outer_surface.m&quot; is not a bash command. Here,  how does it invoke the Matlab?<br>
<br>Any help is greatly appreciated!
<br>
<br>Best wishes,<br><br clear="all">/mnt/freesurfer/subjects$ recon-all -s dinghai_4 -localGI<br>Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0<br>Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0<br>INFO: SUBJECTS_DIR is /mnt/freesurfer/subjects<br>

Actual FREESURFER_HOME /usr/local/freesurfer<br>-rw-rw-r-- 1 huiguang huiguang 803627 Aug 25 09:44 /mnt/freesurfer/subjects/dinghai_4/scripts/recon-all.log<br>Linux hhg-linux 2.6.24-19-generic #1 SMP Wed Aug 20 22:56:21 UTC 2008 i686 GNU/Linux<br>

/mnt/freesurfer/subjects/dinghai_4/surf<br>#--------------------------------------------<br>#@# Local Gyrification Index lh Tue Aug 25 09:54:08 CST 2009<br><br> mris_compute_lgi --i lh.pial <br><br>=================<br>rm -Rf /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial<br>

=================<br>=================<br>mkdir -p /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial<br>=================<br>=================<br>mris_fill -c -r 1 lh.pial /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz<br>

=================<br>reading surface from lh.pial...<br>writing filled volume to /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...<br>conforming output volume<br>setting resolution for intermediate calculations to 1.0000<br>

=================<br>make_outer_surface(&#39;/mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz&#39;,15,&#39;/mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer&#39;); exit<br>

=================<br>if: Expression Syntax.<br><br>ERROR: make_outer_surface did not create output file &#39;/mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer&#39;!<br>Linux hhg-linux 2.6.24-19-generic #1 SMP Wed Aug 20 22:56:21 UTC 2008 i686 GNU/Linux<br>

<br>recon-all exited with ERRORS at Tue Aug 25 09:54:18 CST 2009<br><br>Then I open the matlab ,there is a warning: &quot;Executing startup failed in matlabrc.&#39;,...<br>                &#39;This indicates a potentially serious problem in your MATLAB setup,&#39;,...<br>

                &#39;which should be resolved as soon as possible. &quot; <br><br><br><br>-- <br>Albert<br>Lab of Complex System and Artificial Intelligence,<br>Institute of Automation,Chinese Academy of Sciences(CASIA)<br>

Beijing, 100190,P.R.CHINA<br><br><br>