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
Martin,
Do you have a Mac intel or PowerPC? I am using Mac Intel, with Matlab 7.3 (release 2007a) and don't get this problem. Just to try, I relaunched the code with Matlab 7.4 (2007b), and got the same problem that you have, so that it should be related to a specificity of the Matlab 7.4 version but I am still not able to figure the reason for it... I'll let you know as soon as I have a response.
Marie
On 23 avr. 08, at 20:10, 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
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
Hi Nick,
I am just giving a try to the new mris_compute_lgi matlab script kindly provided by Marie, and so far so good. I would appreciate the new binary for: Mac OS X 10.5.2, linux_x86, and linux_x86_64.
Thanks a lot.
Martin
On Thursday 24 April 2008 18:40:12 Nick Schmansky wrote:
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
Martin,
The binary mris_fill for these OSs can be downloaded from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable
Nick
On Thu, 2008-04-24 at 20:43 +0200, Martin Kavec wrote:
Hi Nick,
I am just giving a try to the new mris_compute_lgi matlab script kindly provided by Marie, and so far so good. I would appreciate the new binary for: Mac OS X 10.5.2, linux_x86, and linux_x86_64.
Thanks a lot.
Martin
On Thursday 24 April 2008 18:40:12 Nick Schmansky wrote:
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
freesurfer@nmr.mgh.harvard.edu
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Marie Schaer -
Martin Kavec -
Nick Schmansky