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.
- 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.
- 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, 2007To 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer