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. "