Hi,everyone.
The debug output is followed. I think the problem is "$MLF | ${MATLAB} -display iconic -nojvm -nosplash"
cat /tmp/mos_12142_.m /usr/local/bin/matlab -display iconic -nojvm -nosplash
this command is not implemented rightly. However, when I run only the matlab cmd, it's seem to be right.
Any help will be appreciated!


huiguang@hhg-linux:/mnt/freesurfer/subjects/dinghai_4/surf$ mris_compute_lgi --i lh.pial --debug
set verbose = 1
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return

goto check_params ;
goto check_params
if ( ! $?FREESURFER_HOME ) then
if ( ! 1 ) then
if ( ! -e $FREESURFER_HOME ) then
if ( ! -e /usr/local/freesurfer ) then
if ( ! $?input ) then
if ( ! 1 ) then
if ( ! -e ${input} ) then
if ( ! -e lh.pial ) then
goto check_params_return ;
goto check_params_return





set MATLAB = `getmatlab` ;
set MATLAB = `getmatlab`
getmatlab
if ( $status ) then
if ( 0 ) then


set tmpdir = ( $PWD/tmp-mris_compute_lgi-${input} )
set tmpdir = ( /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial )
set cmd= ( rm -Rf $tmpdir )
set cmd= ( rm -Rf /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial )
echo "================="
echo =================
=================
echo "$cmd"
echo rm -Rf /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial
rm -Rf /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial
echo "================="
echo =================
=================
if ( $RunIt ) $cmd
if ( 1 ) rm -Rf /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial
rm -Rf /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial
set cmd= ( mkdir -p $tmpdir )
set cmd= ( mkdir -p /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial )
echo "================="
echo =================
=================
echo "$cmd"
echo mkdir -p /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
echo "================="
echo =================
=================
if ( $RunIt ) $cmd
if ( 1 ) mkdir -p /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





set cmd= ( mris_fill -c -r 1 ${input} ${tmpdir}/${input}.filled.mgz )
set cmd= ( mris_fill -c -r 1 lh.pial /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz )
echo "================="
echo =================
=================
echo "$cmd"
echo mris_fill -c -r 1 lh.pial /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
mris_fill -c -r 1 lh.pial /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
echo "================="
echo =================
=================
if ( $RunIt ) $cmd
if ( 1 ) mris_fill -c -r 1 lh.pial /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
mris_fill -c -r 1 lh.pial /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
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...
if ( $status ) then
if ( 0 ) then





set MLF = /tmp/mos"_$$_".m
set MLF = /tmp/mos_12142_.m
set arg1 = ${tmpdir}/${input}.filled.mgz
set arg1 = /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
set arg2 = ${closespheresize}
set arg2 = 15
set arg3 = ${tmpdir}/${input}-outer
set arg3 = /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer
rm -f ${arg3}
rm -f /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer
echo "make_outer_surface('${arg1}',${arg2},'${arg3}'); exit" > $MLF
echo 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
echo "================="
echo =================
=================
echo "`cat $MLF`"
echo `cat /tmp/mos_12142_.m`
cat /tmp/mos_12142_.m
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
echo "================="
echo =================
=================
if ( $RunIt ) then
if ( 1 ) then
cat $MLF | ${MATLAB} -display iconic -nojvm -nosplash
cat /tmp/mos_12142_.m
/usr/local/bin/matlab -display iconic -nojvm -nosplash
if: Expression Syntax.
endif
endif
echo ""
echo

rm -f ${MLF}
rm -f /tmp/mos_12142_.m
if ( $RunIt && ! -e ${arg3} ) then
if ( 1 && ! -e /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer ) then
echo "ERROR: make_outer_surface did not create output file '${arg3}'!"
echo ERROR: make_outer_surface did not create output file '/mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!
ERROR: make_outer_surface did not create output file '/mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!
exit 1
exit 1


huiguang@hhg-linux:/mnt/freesurfer/subjects/dinghai_4/surf$ /usr/local/bin/matlab -display iconic -nojvm -nosplash
Warning: Unable to open display iconic, MATLAB is starting without a display.
  You will not be able to display graphics on the screen.

                              < M A T L A B >
                  Copyright 1984-2007 The MathWorks, Inc.
                         Version 7.4.0.336 (R2007a)
                              January 29, 2007

Warning: Duplicate directory name: /home/huiguang/matlab.
 
  To get started, type one of these: helpwin, helpdesk, or demo.
  For product information, visit www.mathworks.com.
 
>>

On Wed, Aug 26, 2009 at 1:52 AM, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote:
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
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




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