Albert,
If I'm reading this correctly, it means it works for you now, as the
output says that it produced lh.pial-outer. Is this correct? I dont
know why it was not working for you.
Nick
On Fri, 2009-08-28 at 14:52 +0800, leemon albert wrote:
> P.S.:
> >> huigu...@hhg-linux:/mnt/freesurfer/subjects/dinghai_4/surf$
> cat /tmp/mos_25794_.m|/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.
>
> >> reading filled volume...
> closing volume...
> morphological closing done.
> writing outer surface...
>
> huigu...@hhg-linux:/mnt/freesurfer/subjects/dinghai_4/surf$ ls
> tmp-mris_compute_lgi-lh.pial/
> lh.pial.filled.mgz lh.pial-outer
>
> On Thu, Aug 27, 2009 at 9:12 PM, leemon albert
> <albertlee...@gmail.com> wrote:
> Hi,everyone.
> The debug output is followed. I think the problem is "$MLF |
> ${MATLAB} -display iconic -nojvm -nosplash"
> cat /tmp/mos_12142_.m /usr/local/bin/matlab -display iconic
> -nojvm -nosplash
> this command is not implemented rightly. However, when I run
> only the matlab cmd, it's seem to be right.
> Any help will be appreciated!
>
>
> huigu...@hhg-linux:/mnt/freesurfer/subjects/dinghai_4/surf$
> 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
>
>
> huigu...@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
> <ni...@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
>
>
>
>
>
>
> --
> 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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