Martin and other -localGI users,
Independent of the matlab problem, there was a bug that was just
discovered, affecting mris_fill, that breaks the -localGI usage. A fix
will be provided (hopefully along with a fix for this matlab problem) in
v4.0.4. If you need to use the -localGI feature, I can provide fixed
binaries as they appear (email me to request these).
Nick
On Wed, 2008-04-23 at 20:10 +0200, Martin Kavec wrote:
> Hello folks,
>
> I am trying -localGI on Mac, with working Matlab2007.
>
> 1. I think that the getmatlab script is not designed to work on Mac out of
> the
> box, since it is not by default in the $PATH, so it could be caught
> by "which". So I uncommented the three lines and set it hard.
>
> 2. That was easy, but now I am stacked with execution, as it seems that the
> script stops after few minutes, after completing the first matlab
> function "make_outer_surface(...)". The outputs are there, in the
> $SUBJECT/surf/tmp.... directory. Here is the output from
>
> recon-all -s $SUBJECT -localGI
>
> set MLF = /tmp/mos"_$$_".m
> set MLF = /tmp/mos_10410_.m
> set arg1 = ${tmpdir}/${input}.filled.mgz
> set arg1 = tmp-mris_compute_lgi/lh.pial.filled.mgz
> set arg2 = ${closespheresize}
> set arg2 = 15
> set arg3 = ${tmpdir}/${input}-outer
> set arg3 = tmp-mris_compute_lgi/lh.pial-outer
> rm -f ${arg3}
> rm -f tmp-mris_compute_lgi/lh.pial-outer
> echo "make_outer_surface('${arg1}',${arg2},'${arg3}')" > $MLF
> echo
> make_outer_surface('tmp-mris_compute_lgi/lh.pial.filled.mgz',15,'tmp-mris_compute_lgi/lh.pial-outer')
> echo "================="
> echo =================
> =================
> echo "`cat $MLF`"
> echo `cat /tmp/mos_10410_.m`
> cat /tmp/mos_10410_.m
> make_outer_surface('tmp-mris_compute_lgi/lh.pial.filled.mgz',15,'tmp-mris_compute_lgi/lh.pial-outer')
> echo "================="
> echo =================
> =================
> if ( $RunIt ) then
> if ( 1 ) then
> cat $MLF | ${MATLAB} -display iconic -nojvm -nosplash
> cat /tmp/mos_10410_.m
> /Applications/Matlab74/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 7.4.0.287 (R2007a)
> January 29, 2007
>
>
> 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...
> >>
>
> After this, the processor goes down and stays like that, nothing is happening.
>
> Thanks for help,
>
> Martin
> _______________________________________________
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> Freesurfer@nmr.mgh.harvard.edu
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>
>
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