External Email - Use Caution
Hi all,
I just switched from FS 5.3 to 6.0 on Gentoo Linux. Previously Freesurfer worked fine under octave setup (as specified here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.h...), but after the update, when I tried testing a MATLAB related function I get an error:
mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0 INFO: Found 2 Non-Null Conditions INFO: Found 3 Delays Condition Weights: 1.00000000000000000000 0 mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat -wdelay 1 0 0 -octave $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ cmtxfile PASAT.sm5.lh/test.mat nconds 2, wcond 1.00000000000000000000 0 ndelays 3, wdelay 1 0 0 ndelays 3, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR: cannot find matlab. Is it in your path? ERROR running mkcontrast mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat -wdelay 1 0 0 -octave Fri Jun 29 21:21:16 CEST 2018
It seems that the environment variable (FS_USE_OCTAVE) is recognized correctly (the function runs with "-octave" flag), but somehow is omitted during execution? What can I do about it?
I checked that v.5.3 used mkcontrast, whereas v.6.0 uses mkcontrast2 which does not seem to support octave? Is it possible to force calling mkcontrast instead of mkcontrast2?
Best regards, Patrycja
External Email - Use Caution
Hi all,
I'll repost - does FSv6 no longer support octave for FS-Fast processing?
Would appreciate clarification on this :) Patrycja
2018-06-29 21:41 GMT+02:00 Patrycja Naumczyk patrycja.naumczyk@gmail.com:
Hi all,
I just switched from FS 5.3 to 6.0 on Gentoo Linux. Previously Freesurfer worked fine under octave setup (as specified here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/ 2012-January/022135.html), but after the update, when I tried testing a MATLAB related function I get an error:
mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0 INFO: Found 2 Non-Null Conditions INFO: Found 3 Delays Condition Weights: 1.00000000000000000000 0 mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat -wdelay 1 0 0 -octave $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ cmtxfile PASAT.sm5.lh/test.mat nconds 2, wcond 1.00000000000000000000 0 ndelays 3, wdelay 1 0 0 ndelays 3, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR: cannot find matlab. Is it in your path? ERROR running mkcontrast mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat -wdelay 1 0 0 -octave Fri Jun 29 21:21:16 CEST 2018
It seems that the environment variable (FS_USE_OCTAVE) is recognized correctly (the function runs with "-octave" flag), but somehow is omitted during execution? What can I do about it?
I checked that v.5.3 used mkcontrast, whereas v.6.0 uses mkcontrast2 which does not seem to support octave? Is it possible to force calling mkcontrast instead of mkcontrast2?
Best regards, Patrycja
Sorry for the delay. I've put a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 copy it to $FREESURFER_HOME/fsfast/bin
On 07/03/2018 12:13 PM, Patrycja Naumczyk wrote:
Hi all,
I'll repost - does FSv6 no longer support octave for FS-Fast processing?
Would appreciate clarification on this :) Patrycja
2018-06-29 21:41 GMT+02:00 Patrycja Naumczyk <patrycja.naumczyk@gmail.com mailto:patrycja.naumczyk@gmail.com>:
Hi all, I just switched from FS 5.3 to 6.0 on Gentoo Linux. Previously Freesurfer worked fine under octave setup (as specified here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>), but after the update, when I tried testing a MATLAB related function I get an error: mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0 INFO: Found 2 Non-Null Conditions INFO: Found 3 Delays Condition Weights: 1.00000000000000000000 0 mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat -wdelay 1 0 0 -octave $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ cmtxfile PASAT.sm5.lh/test.mat nconds 2, wcond 1.00000000000000000000 0 ndelays 3, wdelay 1 0 0 ndelays 3, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR: cannot find matlab. Is it in your path? ERROR running mkcontrast mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat -wdelay 1 0 0 -octave Fri Jun 29 21:21:16 CEST 2018 It seems that the environment variable (FS_USE_OCTAVE) is recognized correctly (the function runs with "-octave" flag), but somehow is omitted during execution? What can I do about it? I checked that v.5.3 used mkcontrast, whereas v.6.0 uses mkcontrast2 which does not seem to support octave? Is it possible to force calling mkcontrast instead of mkcontrast2? Best regards, Patrycja
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Douglas,
thanks a lot - unfortunately this still doesn't work - it stops at the same cause:
mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0 INFO: Found 2 Non-Null Conditions INFO: Found 3 Delays Condition Weights: 1.00000000000000000000 0 mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat -wdelay 1 0 0 -octave $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ cmtxfile PASAT.sm5.lh/test.mat nconds 2, wcond 1.00000000000000000000 0 ndelays 3, wdelay 1 0 0 ndelays 3, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR: cannot find matlab. Is it in your path? ERROR running mkcontrast mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat -wdelay 1 0 0 -octave Tue Jul 3 18:52:59 CEST 2018
which is apparently when verifying the $FS_MKCON_USE_BIN ? I don't have such a variable (I believe it wasn't necessary with v5.3?). Looking for it I found that a bunch of environment variables are advised in the new FS tutorial (http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup). I should probably update the .bashrc file, but I would like to clarify: 1. Are all of variables mentioned below needed for proper v6.0 FS-Fast functioning or are some of them needed only for course settings?
FS_SPMREG_USE_BIN FS_MKCON_USE_BIN FS_SXA3_USE_BIN
2. To use octave instead of MATLAB - only the $FS_MKCON_USE_BIN should be set to '0', or should I change any of the other two? 3. If all three are needed - what do the $FS_SPMREG_USE_BIN and $FS_SXA3_USE_BIN stand for? 4. Are there any other environment variables that differ between the v.5.3 and v6.0 that I should also add?
Best regards, Patrycja
2018-07-03 18:31 GMT+02:00 Douglas N. Greve dgreve@mgh.harvard.edu:
Sorry for the delay. I've put a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 copy it to $FREESURFER_HOME/fsfast/bin
On 07/03/2018 12:13 PM, Patrycja Naumczyk wrote:
Hi all,
I'll repost - does FSv6 no longer support octave for FS-Fast processing?
Would appreciate clarification on this :) Patrycja
2018-06-29 21:41 GMT+02:00 Patrycja Naumczyk <patrycja.naumczyk@gmail.com mailto:patrycja.naumczyk@gmail.com>:
Hi all, I just switched from FS 5.3 to 6.0 on Gentoo Linux. Previously Freesurfer worked fine under octave setup (as specified here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html
<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>),
but after the update, when I tried testing a MATLAB related function I get an error: mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0 INFO: Found 2 Non-Null Conditions INFO: Found 3 Delays Condition Weights: 1.00000000000000000000 0 mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat -wdelay 1 0 0 -octave $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ cmtxfile PASAT.sm5.lh/test.mat nconds 2, wcond 1.00000000000000000000 0 ndelays 3, wdelay 1 0 0 ndelays 3, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR: cannot find matlab. Is it in your path? ERROR running mkcontrast mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat -wdelay 1 0 0 -octave Fri Jun 29 21:21:16 CEST 2018 It seems that the environment variable (FS_USE_OCTAVE) is recognized correctly (the function runs with "-octave" flag), but somehow is omitted during execution? What can I do about it? I checked that v.5.3 used mkcontrast, whereas v.6.0 uses mkcontrast2 which does not seem to support octave? Is it possible to force calling mkcontrast instead of mkcontrast2? Best regards, Patrycja
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
questions answered below
On 07/03/2018 01:14 PM, Patrycja Naumczyk wrote:
External Email - Use Caution
Douglas,
thanks a lot - unfortunately this still doesn't work - it stops at the same cause:
mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0 INFO: Found 2 Non-Null Conditions INFO: Found 3 Delays Condition Weights: 1.00000000000000000000 0 mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat -wdelay 1 0 0 -octave $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ cmtxfile PASAT.sm5.lh/test.mat nconds 2, wcond 1.00000000000000000000 0 ndelays 3, wdelay 1 0 0 ndelays 3, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR: cannot find matlab. Is it in your path? ERROR running mkcontrast mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat -wdelay 1 0 0 -octave Tue Jul 3 18:52:59 CEST 2018
which is apparently when verifying the $FS_MKCON_USE_BIN ? I don't have such a variable (I believe it wasn't necessary with v5.3?). Looking for it I found that a bunch of environment variables are advised in the new FS tutorial (http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup). I should probably update the .bashrc file, but I would like to clarify:
- Are all of variables mentioned below needed for proper v6.0 FS-Fast
functioning or are some of them needed only for course settings? FS_SPMREG_USE_BIN FS_MKCON_USE_BIN FS_SXA3_USE_BIN
These are only needed if you want to use the matlab binaries
- To use octave instead of MATLAB - only the $FS_MKCON_USE_BIN should
be set to '0', or should I change any of the other two?
Just FS_MKCON_USE_BIN(or leave it undefined).
- If all three are needed - what do the $FS_SPMREG_USE_BIN and
$FS_SXA3_USE_BIN stand for?
These are to use the matlab binaries when running these programs (binaries don't require a license). We do not use spm for registration anymore, so that this irrelevant. SXA3 refers to selxavg3-sess.
- Are there any other environment variables that differ between the
v.5.3 and v6.0 that I should also add?
I don't think so.
Best regards, Patrycja
2018-07-03 18:31 GMT+02:00 Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>:
Sorry for the delay. I've put a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2> copy it to $FREESURFER_HOME/fsfast/bin On 07/03/2018 12:13 PM, Patrycja Naumczyk wrote: > > > Hi all, > > I'll repost - does FSv6 no longer support octave for FS-Fast processing? > > Would appreciate clarification on this :) > Patrycja > > 2018-06-29 21:41 GMT+02:00 Patrycja Naumczyk > <patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>>>: > > Hi all, > > I just switched from FS 5.3 to 6.0 on Gentoo Linux. Previously > Freesurfer worked fine under octave setup (as specified here: > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html> > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>>), > but after the update, when I tried testing a MATLAB related > function I get an error: > > mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0 > INFO: Found 2 Non-Null Conditions > INFO: Found 3 Delays > Condition Weights: 1.00000000000000000000 0 > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh > -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat > -wdelay 1 0 0 -octave > $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ > cmtxfile PASAT.sm5.lh/test.mat > nconds 2, wcond 1.00000000000000000000 0 > ndelays 3, wdelay 1 0 0 > ndelays 3, wpsa > sumconds 1 > sumdelays 0 > nircorr 0 > TER 0.050000 > rdelta > rtau > ERROR: cannot find matlab. Is it in your path? > ERROR running mkcontrast > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh > -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat > -wdelay 1 0 0 -octave > Fri Jun 29 21:21:16 CEST 2018 > > It seems that the environment variable (FS_USE_OCTAVE) is > recognized correctly (the function runs with "-octave" flag), but > somehow is omitted during execution? What can I do about it? > > I checked that v.5.3 used mkcontrast, whereas v.6.0 uses > mkcontrast2 which does not seem to support octave? Is it possible > to force calling mkcontrast instead of mkcontrast2? > > Best regards, > Patrycja > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Douglas,
thank you for clarifying. The problem is that both when $FS_MKCON_USE_BIN is not defined and when it is set to '0' mkcontrast2 asks for MATLAB path (as in my previous mail). What should I do to make it use octave instead?
Best regards, Patrycja
2018-07-03 19:23 GMT+02:00 Douglas N. Greve dgreve@mgh.harvard.edu:
questions answered below
On 07/03/2018 01:14 PM, Patrycja Naumczyk wrote:
External Email - Use CautionDouglas,
thanks a lot - unfortunately this still doesn't work - it stops at the same cause:
mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0 INFO: Found 2 Non-Null Conditions INFO: Found 3 Delays Condition Weights: 1.00000000000000000000 0 mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat -wdelay 1 0 0 -octave $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ cmtxfile PASAT.sm5.lh/test.mat nconds 2, wcond 1.00000000000000000000 0 ndelays 3, wdelay 1 0 0 ndelays 3, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR: cannot find matlab. Is it in your path? ERROR running mkcontrast mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat -wdelay 1 0 0 -octave Tue Jul 3 18:52:59 CEST 2018
which is apparently when verifying the $FS_MKCON_USE_BIN ? I don't have such a variable (I believe it wasn't necessary with v5.3?). Looking for it I found that a bunch of environment variables are advised in the new FS tutorial (http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup). I should probably update the .bashrc file, but I would like to clarify:
- Are all of variables mentioned below needed for proper v6.0 FS-Fast
functioning or are some of them needed only for course settings? FS_SPMREG_USE_BIN FS_MKCON_USE_BIN FS_SXA3_USE_BIN
These are only needed if you want to use the matlab binaries
- To use octave instead of MATLAB - only the $FS_MKCON_USE_BIN should
be set to '0', or should I change any of the other two?
Just FS_MKCON_USE_BIN(or leave it undefined).
- If all three are needed - what do the $FS_SPMREG_USE_BIN and
$FS_SXA3_USE_BIN stand for?
These are to use the matlab binaries when running these programs (binaries don't require a license). We do not use spm for registration anymore, so that this irrelevant. SXA3 refers to selxavg3-sess.
- Are there any other environment variables that differ between the
v.5.3 and v6.0 that I should also add?
I don't think so.
Best regards, Patrycja
2018-07-03 18:31 GMT+02:00 Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>:
Sorry for the delay. I've put a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2> copy it to $FREESURFER_HOME/fsfast/bin On 07/03/2018 12:13 PM, Patrycja Naumczyk wrote: > > > Hi all, > > I'll repost - does FSv6 no longer support octave for FS-Fast processing? > > Would appreciate clarification on this :) > Patrycja > > 2018-06-29 21:41 GMT+02:00 Patrycja Naumczyk > <patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>>>: > > Hi all, > > I just switched from FS 5.3 to 6.0 on Gentoo Linux. Previously > Freesurfer worked fine under octave setup (as specified here: > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html
<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>
> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html
<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>>),
> but after the update, when I tried testing a MATLAB related > function I get an error: > > mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0 > INFO: Found 2 Non-Null Conditions > INFO: Found 3 Delays > Condition Weights: 1.00000000000000000000 0 > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh > -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat > -wdelay 1 0 0 -octave > $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ > cmtxfile PASAT.sm5.lh/test.mat > nconds 2, wcond 1.00000000000000000000 0 > ndelays 3, wdelay 1 0 0 > ndelays 3, wpsa > sumconds 1 > sumdelays 0 > nircorr 0 > TER 0.050000 > rdelta > rtau > ERROR: cannot find matlab. Is it in your path? > ERROR running mkcontrast > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh > -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat > -wdelay 1 0 0 -octave > Fri Jun 29 21:21:16 CEST 2018 > > It seems that the environment variable (FS_USE_OCTAVE) is > recognized correctly (the function runs with "-octave" flag), but > somehow is omitted during execution? What can I do about it? > > I checked that v.5.3 used mkcontrast, whereas v.6.0 uses > mkcontrast2 which does not seem to support octave? Is it possible > to force calling mkcontrast instead of mkcontrast2? > > Best regards, > Patrycja > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Are you sure you're using the new one? I've tested it on my system, and it works.
On 07/03/2018 01:33 PM, Patrycja Naumczyk wrote:
External Email - Use Caution
Douglas,
thank you for clarifying. The problem is that both when $FS_MKCON_USE_BIN is not defined and when it is set to '0' mkcontrast2 asks for MATLAB path (as in my previous mail). What should I do to make it use octave instead?
Best regards, Patrycja
2018-07-03 19:23 GMT+02:00 Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>:
questions answered below On 07/03/2018 01:14 PM, Patrycja Naumczyk wrote: > > External Email - Use Caution > > Douglas, > > thanks a lot - unfortunately this still doesn't work - it stops at the > same cause: > > mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0 > INFO: Found 2 Non-Null Conditions > INFO: Found 3 Delays > Condition Weights: 1.00000000000000000000 0 > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh > -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat > -wdelay 1 0 0 -octave > $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ > cmtxfile PASAT.sm5.lh/test.mat > nconds 2, wcond 1.00000000000000000000 0 > ndelays 3, wdelay 1 0 0 > ndelays 3, wpsa > sumconds 1 > sumdelays 0 > nircorr 0 > TER 0.050000 > rdelta > rtau > ERROR: cannot find matlab. Is it in your path? > ERROR running mkcontrast > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh > -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat > -wdelay 1 0 0 -octave > Tue Jul 3 18:52:59 CEST 2018 > > which is apparently when verifying the $FS_MKCON_USE_BIN ? I don't > have such a variable (I believe it wasn't necessary with v5.3?). > Looking for it I found that a bunch of environment variables are > advised in the new FS tutorial > (http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup <http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup>). I should > probably update the .bashrc file, but I would like to clarify: > 1. Are all of variables mentioned below needed for proper v6.0 FS-Fast > functioning or are some of them needed only for course settings? > FS_SPMREG_USE_BIN > FS_MKCON_USE_BIN > FS_SXA3_USE_BIN These are only needed if you want to use the matlab binaries > 2. To use octave instead of MATLAB - only the $FS_MKCON_USE_BIN should > be set to '0', or should I change any of the other two? Just FS_MKCON_USE_BIN(or leave it undefined). > 3. If all three are needed - what do the $FS_SPMREG_USE_BIN and > $FS_SXA3_USE_BIN stand for? These are to use the matlab binaries when running these programs (binaries don't require a license). We do not use spm for registration anymore, so that this irrelevant. SXA3 refers to selxavg3-sess. > 4. Are there any other environment variables that differ between the > v.5.3 and v6.0 that I should also add? I don't think so. > > Best regards, > Patrycja > > > > 2018-07-03 18:31 GMT+02:00 Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>>: > > Sorry for the delay. I've put a new version here > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2> > <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2>> > copy it to $FREESURFER_HOME/fsfast/bin > > > > > On 07/03/2018 12:13 PM, Patrycja Naumczyk wrote: > > > > > > Hi all, > > > > I'll repost - does FSv6 no longer support octave for FS-Fast > processing? > > > > Would appreciate clarification on this :) > > Patrycja > > > > 2018-06-29 21:41 GMT+02:00 Patrycja Naumczyk > > <patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>>>>: > > > > Hi all, > > > > I just switched from FS 5.3 to 6.0 on Gentoo Linux. Previously > > Freesurfer worked fine under octave setup (as specified here: > > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html> > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>> > > > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html> > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>>>), > > but after the update, when I tried testing a MATLAB related > > function I get an error: > > > > mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0 > > INFO: Found 2 Non-Null Conditions > > INFO: Found 3 Delays > > Condition Weights: 1.00000000000000000000 0 > > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir > PASAT.sm5.lh > > -wcond 1.00000000000000000000 0 -sumconds -o > PASAT.sm5.lh/test.mat > > -wdelay 1 0 0 -octave > > $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ > > cmtxfile PASAT.sm5.lh/test.mat > > nconds 2, wcond 1.00000000000000000000 0 > > ndelays 3, wdelay 1 0 0 > > ndelays 3, wpsa > > sumconds 1 > > sumdelays 0 > > nircorr 0 > > TER 0.050000 > > rdelta > > rtau > > ERROR: cannot find matlab. Is it in your path? > > ERROR running mkcontrast > > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir > PASAT.sm5.lh > > -wcond 1.00000000000000000000 0 -sumconds -o > PASAT.sm5.lh/test.mat > > -wdelay 1 0 0 -octave > > Fri Jun 29 21:21:16 CEST 2018 > > > > It seems that the environment variable (FS_USE_OCTAVE) is > > recognized correctly (the function runs with "-octave" > flag), but > > somehow is omitted during execution? What can I do about it? > > > > I checked that v.5.3 used mkcontrast, whereas v.6.0 uses > > mkcontrast2 which does not seem to support octave? Is it > possible > > to force calling mkcontrast instead of mkcontrast2? > > > > Best regards, > > Patrycja > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> . If the e-mail was sent > to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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External Email - Use Caution
OK - I double checked, and even compared the new mkcontrast2 with the old one to verify that I copied all as I should (see below). Still the mkcontrast2 exits when checking $FS_MKCON_USE_BIN with the same error message (no matter if this variable is undefined or is it defined and set to zero):
ERROR: cannot find matlab. Is it in your path? ERROR running mkcontrast
'diff' output (new > old):
57,163c157 < if($UseOctave == 0) then < echo "------- matlab output --------------------"
< cat $mfile | $MATLAB -nosplash -display iconic -nodesktop < else
< echo "------- octave output --------------------"
< cat $mfile | octave
< endif
---
cat $mfile | $MATLAB -nosplash -display iconic
-nodesktop 447a442,466
if($UseOctave)
then
if($?FS_OCTAVE_LIB == 0)
then
echo "ERROR: you must set the FS_OCTAVE_LIB environment
variable"
exit
1;
endif
if(! -e $FS_OCTAVE_LIB)
then
echo "ERROR: cannot find
$FS_OCTAVE_LIB"
exit
1;
endif
if($?FS_OCTAVE_BIN == 0)
then
echo "ERROR: you must set the FS_OCTAVE_BIN environment variable" exit 1; endif if(! -x $FS_OCTAVE_BIN) then echo "ERROR: cannot find or execute $FS_OCTAVE_BIN" exit 1; endif if($?LD_LIBRARY_PATH == 0) setenv LD_LIBRARY_PATH "" if($#LD_LIBRARY_PATH == 0) then setenv LD_LIBRARY_PATH $FS_OCTAVE_LIB else setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:$FS_OCTAVE_LIB endifendif
470a490
Probably I am omitting something, but I have no clue what is the problem here :/
Patrycja
2018-07-03 19:35 GMT+02:00 Douglas N. Greve dgreve@mgh.harvard.edu:
Are you sure you're using the new one? I've tested it on my system, and it works.
On 07/03/2018 01:33 PM, Patrycja Naumczyk wrote:
External Email - Use CautionDouglas,
thank you for clarifying. The problem is that both when $FS_MKCON_USE_BIN is not defined and when it is set to '0' mkcontrast2 asks for MATLAB path (as in my previous mail). What should I do to make it use octave instead?
Best regards, Patrycja
2018-07-03 19:23 GMT+02:00 Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>:
questions answered below On 07/03/2018 01:14 PM, Patrycja Naumczyk wrote: > > External Email - Use Caution > > Douglas, > > thanks a lot - unfortunately this still doesn't work - it stops at the > same cause: > > mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0 > INFO: Found 2 Non-Null Conditions > INFO: Found 3 Delays > Condition Weights: 1.00000000000000000000 0 > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh > -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat > -wdelay 1 0 0 -octave > $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ > cmtxfile PASAT.sm5.lh/test.mat > nconds 2, wcond 1.00000000000000000000 0 > ndelays 3, wdelay 1 0 0 > ndelays 3, wpsa > sumconds 1 > sumdelays 0 > nircorr 0 > TER 0.050000 > rdelta > rtau > ERROR: cannot find matlab. Is it in your path? > ERROR running mkcontrast > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh > -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat > -wdelay 1 0 0 -octave > Tue Jul 3 18:52:59 CEST 2018 > > which is apparently when verifying the $FS_MKCON_USE_BIN ? I don't > have such a variable (I believe it wasn't necessary with v5.3?). > Looking for it I found that a bunch of environment variables are > advised in the new FS tutorial > (http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup <http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup>). I should > probably update the .bashrc file, but I would like to clarify: > 1. Are all of variables mentioned below needed for proper v6.0 FS-Fast > functioning or are some of them needed only for course settings? > FS_SPMREG_USE_BIN > FS_MKCON_USE_BIN > FS_SXA3_USE_BIN These are only needed if you want to use the matlab binaries > 2. To use octave instead of MATLAB - only the $FS_MKCON_USE_BINshould
> be set to '0', or should I change any of the other two? Just FS_MKCON_USE_BIN(or leave it undefined). > 3. If all three are needed - what do the $FS_SPMREG_USE_BIN and > $FS_SXA3_USE_BIN stand for? These are to use the matlab binaries when running these programs (binaries don't require a license). We do not use spm for registration anymore, so that this irrelevant. SXA3 refers to selxavg3-sess. > 4. Are there any other environment variables that differ betweenthe
> v.5.3 and v6.0 that I should also add? I don't think so. > > Best regards, > Patrycja > > > > 2018-07-03 18:31 GMT+02:00 Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>>: > > Sorry for the delay. I've put a new version here > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2> > <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2>> > copy it to $FREESURFER_HOME/fsfast/bin > > > > > On 07/03/2018 12:13 PM, Patrycja Naumczyk wrote: > > > > > > Hi all, > > > > I'll repost - does FSv6 no longer support octave for FS-Fast > processing? > > > > Would appreciate clarification on this :) > > Patrycja > > > > 2018-06-29 21:41 GMT+02:00 Patrycja Naumczyk > > <patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>>>>: > > > > Hi all, > > > > I just switched from FS 5.3 to 6.0 on Gentoo Linux. Previously > > Freesurfer worked fine under octave setup (as specified here: > > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html
<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>
> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html
<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>>
> > > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html
<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>
> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html
<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>>>),
> > but after the update, when I tried testing a MATLAB related > > function I get an error: > > > > mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0 > > INFO: Found 2 Non-Null Conditions > > INFO: Found 3 Delays > > Condition Weights: 1.00000000000000000000 0 > > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir > PASAT.sm5.lh > > -wcond 1.00000000000000000000 0 -sumconds -o > PASAT.sm5.lh/test.mat > > -wdelay 1 0 0 -octave > > $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ > > cmtxfile PASAT.sm5.lh/test.mat > > nconds 2, wcond 1.00000000000000000000 0 > > ndelays 3, wdelay 1 0 0 > > ndelays 3, wpsa > > sumconds 1 > > sumdelays 0 > > nircorr 0 > > TER 0.050000 > > rdelta > > rtau > > ERROR: cannot find matlab. Is it in your path? > > ERROR running mkcontrast > > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir > PASAT.sm5.lh > > -wcond 1.00000000000000000000 0 -sumconds -o > PASAT.sm5.lh/test.mat > > -wdelay 1 0 0 -octave > > Fri Jun 29 21:21:16 CEST 2018 > > > > It seems that the environment variable (FS_USE_OCTAVE) is > > recognized correctly (the function runs with "-octave" > flag), but > > somehow is omitted during execution? What can I do about it? > > > > I checked that v.5.3 used mkcontrast, whereas v.6.0 uses > > mkcontrast2 which does not seem to support octave? Is it > possible > > to force calling mkcontrast instead of mkcontrast2? > > > > Best regards, > > Patrycja > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> . If the e-mail was sent > to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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External Email - Use Caution
Hi Doug,
I walked through the mkcontrast2 and found it failed when executing the loop below:
if($FS_MKCON_USE_BIN == 0) then set MATLAB = `getmatlab`; if($status) then echo "ERROR: cannot find matlab. Is it in your path?" exit 1; endif endif
I changed the clause to if($FS_MKCON_USE_BIN == 1) as to me it didn't make sense to verify if you can find matlab in the path, when the $FS_MKCON_USE_BIN is set to 0. Now it works OK, and creates the contrast files as it should via octave.
Best regards, Patrycja
2018-07-03 21:48 GMT+02:00 Patrycja Naumczyk patrycja.naumczyk@gmail.com:
OK - I double checked, and even compared the new mkcontrast2 with the old one to verify that I copied all as I should (see below). Still the mkcontrast2 exits when checking $FS_MKCON_USE_BIN with the same error message (no matter if this variable is undefined or is it defined and set to zero):
ERROR: cannot find matlab. Is it in your path? ERROR running mkcontrast
'diff' output (new > old):
57,163c157 < if($UseOctave == 0) then < echo "------- matlab output --------------------"
< cat $mfile | $MATLAB -nosplash -display iconic -nodesktop < else
< echo "------- octave output --------------------"
< cat $mfile | octave
< endif
cat $mfile | $MATLAB -nosplash -display iconic
-nodesktop 447a442,466
if($UseOctave) then
if($?FS_OCTAVE_LIB == 0) thenecho "ERROR: you must set the FS_OCTAVE_LIB environmentvariable"
exit 1;endifif(! -e $FS_OCTAVE_LIB) thenecho "ERROR: cannot find $FS_OCTAVE_LIB"exit 1;endifif($?FS_OCTAVE_BIN == 0) thenecho "ERROR: you must set the FS_OCTAVE_BIN environment variable" exit 1; endif if(! -x $FS_OCTAVE_BIN) then echo "ERROR: cannot find or execute $FS_OCTAVE_BIN" exit 1; endif if($?LD_LIBRARY_PATH == 0) setenv LD_LIBRARY_PATH "" if($#LD_LIBRARY_PATH == 0) then setenv LD_LIBRARY_PATH $FS_OCTAVE_LIB else setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:$FS_OCTAVE_LIB endifendif
470a490
Probably I am omitting something, but I have no clue what is the problem here :/
Patrycja
2018-07-03 19:35 GMT+02:00 Douglas N. Greve dgreve@mgh.harvard.edu:
Are you sure you're using the new one? I've tested it on my system, and it works.
On 07/03/2018 01:33 PM, Patrycja Naumczyk wrote:
External Email - Use CautionDouglas,
thank you for clarifying. The problem is that both when $FS_MKCON_USE_BIN is not defined and when it is set to '0' mkcontrast2 asks for MATLAB path (as in my previous mail). What should I do to make it use octave instead?
Best regards, Patrycja
2018-07-03 19:23 GMT+02:00 Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>:
questions answered below On 07/03/2018 01:14 PM, Patrycja Naumczyk wrote: > > External Email - Use Caution > > Douglas, > > thanks a lot - unfortunately this still doesn't work - it stops at the > same cause: > > mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0 > INFO: Found 2 Non-Null Conditions > INFO: Found 3 Delays > Condition Weights: 1.00000000000000000000 0 > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh > -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat > -wdelay 1 0 0 -octave > $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ > cmtxfile PASAT.sm5.lh/test.mat > nconds 2, wcond 1.00000000000000000000 0 > ndelays 3, wdelay 1 0 0 > ndelays 3, wpsa > sumconds 1 > sumdelays 0 > nircorr 0 > TER 0.050000 > rdelta > rtau > ERROR: cannot find matlab. Is it in your path? > ERROR running mkcontrast > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh > -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat > -wdelay 1 0 0 -octave > Tue Jul 3 18:52:59 CEST 2018 > > which is apparently when verifying the $FS_MKCON_USE_BIN ? I don't > have such a variable (I believe it wasn't necessary with v5.3?). > Looking for it I found that a bunch of environment variables are > advised in the new FS tutorial > (http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup <http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup>). I should > probably update the .bashrc file, but I would like to clarify: > 1. Are all of variables mentioned below needed for proper v6.0 FS-Fast > functioning or are some of them needed only for course settings? > FS_SPMREG_USE_BIN > FS_MKCON_USE_BIN > FS_SXA3_USE_BIN These are only needed if you want to use the matlab binaries > 2. To use octave instead of MATLAB - only the $FS_MKCON_USE_BINshould
> be set to '0', or should I change any of the other two? Just FS_MKCON_USE_BIN(or leave it undefined). > 3. If all three are needed - what do the $FS_SPMREG_USE_BIN and > $FS_SXA3_USE_BIN stand for? These are to use the matlab binaries when running these programs (binaries don't require a license). We do not use spm for registration anymore, so that this irrelevant. SXA3 refers to selxavg3-sess. > 4. Are there any other environment variables that differ betweenthe
> v.5.3 and v6.0 that I should also add? I don't think so. > > Best regards, > Patrycja > > > > 2018-07-03 18:31 GMT+02:00 Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>>: > > Sorry for the delay. I've put a new version here > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2> > <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2>> > copy it to $FREESURFER_HOME/fsfast/bin > > > > > On 07/03/2018 12:13 PM, Patrycja Naumczyk wrote: > > > > > > Hi all, > > > > I'll repost - does FSv6 no longer support octave for FS-Fast > processing? > > > > Would appreciate clarification on this :) > > Patrycja > > > > 2018-06-29 21:41 GMT+02:00 Patrycja Naumczyk > > <patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>>>>: > > > > Hi all, > > > > I just switched from FS 5.3 to 6.0 on Gentoo Linux. Previously > > Freesurfer worked fine under octave setup (as specified here: > > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html
<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>
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<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>>
> > > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html
<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>
> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html
<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>>>),
> > but after the update, when I tried testing a MATLAB related > > function I get an error: > > > > mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0 > > INFO: Found 2 Non-Null Conditions > > INFO: Found 3 Delays > > Condition Weights: 1.00000000000000000000 0 > > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir > PASAT.sm5.lh > > -wcond 1.00000000000000000000 0 -sumconds -o > PASAT.sm5.lh/test.mat > > -wdelay 1 0 0 -octave > > $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ > > cmtxfile PASAT.sm5.lh/test.mat > > nconds 2, wcond 1.00000000000000000000 0 > > ndelays 3, wdelay 1 0 0 > > ndelays 3, wpsa > > sumconds 1 > > sumdelays 0 > > nircorr 0 > > TER 0.050000 > > rdelta > > rtau > > ERROR: cannot find matlab. Is it in your path? > > ERROR running mkcontrast > > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir > PASAT.sm5.lh > > -wcond 1.00000000000000000000 0 -sumconds -o > PASAT.sm5.lh/test.mat > > -wdelay 1 0 0 -octave > > Fri Jun 29 21:21:16 CEST 2018 > > > > It seems that the environment variable (FS_USE_OCTAVE)is
> > recognized correctly (the function runs with "-octave" > flag), but > > somehow is omitted during execution? What can I do about it? > > > > I checked that v.5.3 used mkcontrast, whereas v.6.0 uses > > mkcontrast2 which does not seem to support octave? Is it > possible > > to force calling mkcontrast instead of mkcontrast2? > > > > Best regards, > > Patrycja > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> . If the e-mail was sent > to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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Oh, I see now. It never failed for me because matlab is defined in my path. I think the right logic is if($FS_MKCON_USE_BIN == 0 && UseOctave == 0) then ...
I've put a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 Can you try it out?
On 07/06/2018 01:20 PM, Patrycja Naumczyk wrote:
External Email - Use Caution
Hi Doug,
I walked through the mkcontrast2 and found it failed when executing the loop below:
if($FS_MKCON_USE_BIN == 0) then set MATLAB = `getmatlab`; if($status) then echo "ERROR: cannot find matlab. Is it in your path?" exit 1; endif endif
I changed the clause to if($FS_MKCON_USE_BIN == 1) as to me it didn't make sense to verify if you can find matlab in the path, when the $FS_MKCON_USE_BIN is set to 0. Now it works OK, and creates the contrast files as it should via octave.
Best regards, Patrycja
2018-07-03 21:48 GMT+02:00 Patrycja Naumczyk <patrycja.naumczyk@gmail.com mailto:patrycja.naumczyk@gmail.com>:
OK - I double checked, and even compared the new mkcontrast2 with the old one to verify that I copied all as I should (see below). Still the mkcontrast2 exits when checking $FS_MKCON_USE_BIN with the same error message (no matter if this variable is undefined or is it defined and set to zero): ERROR: cannot find matlab. Is it in your path? ERROR running mkcontrast 'diff' output (new > old): 57,163c157 < if($UseOctave == 0) then < echo "------- matlab output --------------------" < cat $mfile | $MATLAB -nosplash -display iconic -nodesktop < else < echo "------- octave output --------------------" < cat $mfile | octave < endif --- > cat $mfile | $MATLAB -nosplash -display iconic -nodesktop 447a442,466 > if($UseOctave) then > if($?FS_OCTAVE_LIB == 0) then > echo "ERROR: you must set the FS_OCTAVE_LIB environment variable" > exit 1; > endif > if(! -e $FS_OCTAVE_LIB) then > echo "ERROR: cannot find $FS_OCTAVE_LIB" > exit 1; > endif > if($?FS_OCTAVE_BIN == 0) then > echo "ERROR: you must set the FS_OCTAVE_BIN environment variable" > exit 1; > endif > if(! -x $FS_OCTAVE_BIN) then > echo "ERROR: cannot find or execute $FS_OCTAVE_BIN" > exit 1; > endif > if($?LD_LIBRARY_PATH == 0) setenv LD_LIBRARY_PATH "" > if($#LD_LIBRARY_PATH == 0) then > setenv LD_LIBRARY_PATH $FS_OCTAVE_LIB > else > setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:$FS_OCTAVE_LIB > endif > endif > 470a490 > Probably I am omitting something, but I have no clue what is the problem here :/ Patrycja 2018-07-03 19:35 GMT+02:00 Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>: Are you sure you're using the new one? I've tested it on my system, and it works. On 07/03/2018 01:33 PM, Patrycja Naumczyk wrote: > > External Email - Use Caution > > Douglas, > > thank you for clarifying. The problem is that both when > $FS_MKCON_USE_BIN is not defined and when it is set to '0' mkcontrast2 > asks for MATLAB path (as in my previous mail). What should I do to > make it use octave instead? > > Best regards, > Patrycja > > 2018-07-03 19:23 GMT+02:00 Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>>: > > questions answered below > > On 07/03/2018 01:14 PM, Patrycja Naumczyk wrote: > > > > External Email - Use Caution > > > > Douglas, > > > > thanks a lot - unfortunately this still doesn't work - it stops > at the > > same cause: > > > > mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0 > > INFO: Found 2 Non-Null Conditions > > INFO: Found 3 Delays > > Condition Weights: 1.00000000000000000000 0 > > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh > > -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat > > -wdelay 1 0 0 -octave > > $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ > > cmtxfile PASAT.sm5.lh/test.mat > > nconds 2, wcond 1.00000000000000000000 0 > > ndelays 3, wdelay 1 0 0 > > ndelays 3, wpsa > > sumconds 1 > > sumdelays 0 > > nircorr 0 > > TER 0.050000 > > rdelta > > rtau > > ERROR: cannot find matlab. Is it in your path? > > ERROR running mkcontrast > > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh > > -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat > > -wdelay 1 0 0 -octave > > Tue Jul 3 18:52:59 CEST 2018 > > > > which is apparently when verifying the $FS_MKCON_USE_BIN ? I don't > > have such a variable (I believe it wasn't necessary with v5.3?). > > Looking for it I found that a bunch of environment variables are > > advised in the new FS tutorial > > (http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup <http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup> > <http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup <http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup>>). I > should > > probably update the .bashrc file, but I would like to clarify: > > 1. Are all of variables mentioned below needed for proper v6.0 > FS-Fast > > functioning or are some of them needed only for course settings? > > FS_SPMREG_USE_BIN > > FS_MKCON_USE_BIN > > FS_SXA3_USE_BIN > These are only needed if you want to use the matlab binaries > > 2. To use octave instead of MATLAB - only the $FS_MKCON_USE_BIN should > > be set to '0', or should I change any of the other two? > Just FS_MKCON_USE_BIN(or leave it undefined). > > 3. If all three are needed - what do the $FS_SPMREG_USE_BIN and > > $FS_SXA3_USE_BIN stand for? > These are to use the matlab binaries when running these programs > (binaries don't require a license). We do not use spm for > registration > anymore, so that this irrelevant. SXA3 refers to selxavg3-sess. > > 4. Are there any other environment variables that differ between the > > v.5.3 and v6.0 that I should also add? > I don't think so. > > > > Best regards, > > Patrycja > > > > > > > > 2018-07-03 18:31 GMT+02:00 Douglas N. Greve > <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> > > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>>>: > > > > Sorry for the delay. I've put a new version here > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2> > <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2>> > > > <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2> > <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2>>> > > copy it to $FREESURFER_HOME/fsfast/bin > > > > > > > > > > On 07/03/2018 12:13 PM, Patrycja Naumczyk wrote: > > > > > > > > > Hi all, > > > > > > I'll repost - does FSv6 no longer support octave for FS-Fast > > processing? > > > > > > Would appreciate clarification on this :) > > > Patrycja > > > > > > 2018-06-29 21:41 GMT+02:00 Patrycja Naumczyk > > > <patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>> > > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>>> > > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>> > > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>>>>>: > > > > > > Hi all, > > > > > > I just switched from FS 5.3 to 6.0 on Gentoo Linux. > Previously > > > Freesurfer worked fine under octave setup (as > specified here: > > > > > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html> > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>> > > > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html> > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>>> > > > > > > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html> > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>> > > > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html> > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>>>>), > > > but after the update, when I tried testing a MATLAB > related > > > function I get an error: > > > > > > mkcontrast-sess -analysis PASAT.sm5.lh -contrast test > -a 1 -c 0 > > > INFO: Found 2 Non-Null Conditions > > > INFO: Found 3 Delays > > > Condition Weights: 1.00000000000000000000 0 > > > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir > > PASAT.sm5.lh > > > -wcond 1.00000000000000000000 0 -sumconds -o > > PASAT.sm5.lh/test.mat > > > -wdelay 1 0 0 -octave > > > $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ > > > cmtxfile PASAT.sm5.lh/test.mat > > > nconds 2, wcond 1.00000000000000000000 0 > > > ndelays 3, wdelay 1 0 0 > > > ndelays 3, wpsa > > > sumconds 1 > > > sumdelays 0 > > > nircorr 0 > > > TER 0.050000 > > > rdelta > > > rtau > > > ERROR: cannot find matlab. Is it in your path? > > > ERROR running mkcontrast > > > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir > > PASAT.sm5.lh > > > -wcond 1.00000000000000000000 0 -sumconds -o > > PASAT.sm5.lh/test.mat > > > -wdelay 1 0 0 -octave > > > Fri Jun 29 21:21:16 CEST 2018 > > > > > > It seems that the environment variable (FS_USE_OCTAVE) is > > > recognized correctly (the function runs with "-octave" > > flag), but > > > somehow is omitted during execution? What can I do > about it? > > > > > > I checked that v.5.3 used mkcontrast, whereas v.6.0 uses > > > mkcontrast2 which does not seem to support octave? Is it > > possible > > > to force calling mkcontrast instead of mkcontrast2? > > > > > > Best regards, > > > Patrycja > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > The information in this e-mail is intended only for the > person to > > whom it is > > addressed. If you believe this e-mail was sent to you in > error and > > the e-mail > > contains patient information, please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>> . If the e-mail was sent > > to you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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Hi Doug,
I've tried the new version You posted - it works fine as well. Many thanks!
Best regards, Patrycja
2018-07-16 19:58 GMT+02:00 Douglas N. Greve dgreve@mgh.harvard.edu:
Oh, I see now. It never failed for me because matlab is defined in my path. I think the right logic is if($FS_MKCON_USE_BIN == 0 && UseOctave == 0) then ...
I've put a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 Can you try it out?
On 07/06/2018 01:20 PM, Patrycja Naumczyk wrote:
External Email - Use CautionHi Doug,
I walked through the mkcontrast2 and found it failed when executing the loop below:
if($FS_MKCON_USE_BIN == 0) then set MATLAB = `getmatlab`; if($status) then echo "ERROR: cannot find matlab. Is it in your path?" exit 1; endif endif
I changed the clause to if($FS_MKCON_USE_BIN == 1) as to me it didn't make sense to verify if you can find matlab in the path, when the $FS_MKCON_USE_BIN is set to 0. Now it works OK, and creates the contrast files as it should via octave.
Best regards, Patrycja
2018-07-03 21:48 GMT+02:00 Patrycja Naumczyk <patrycja.naumczyk@gmail.com mailto:patrycja.naumczyk@gmail.com>:
OK - I double checked, and even compared the new mkcontrast2 with the old one to verify that I copied all as I should (see below). Still the mkcontrast2 exits when checking $FS_MKCON_USE_BIN with the same error message (no matter if this variable is undefined or is it defined and set to zero): ERROR: cannot find matlab. Is it in your path? ERROR running mkcontrast 'diff' output (new > old): 57,163c157 < if($UseOctave == 0) then < echo "------- matlab output --------------------" < cat $mfile | $MATLAB -nosplash -display iconic -nodesktop < else < echo "------- octave output --------------------" < cat $mfile | octave < endif --- > cat $mfile | $MATLAB -nosplash -display iconic -nodesktop 447a442,466 > if($UseOctave) then > if($?FS_OCTAVE_LIB == 0) then > echo "ERROR: you must set the FS_OCTAVE_LIB environment variable" > exit 1; > endif > if(! -e $FS_OCTAVE_LIB) then > echo "ERROR: cannot find $FS_OCTAVE_LIB" > exit 1; > endif > if($?FS_OCTAVE_BIN == 0) then > echo "ERROR: you must set the FS_OCTAVE_BIN environment variable" > exit 1; > endif > if(! -x $FS_OCTAVE_BIN) then > echo "ERROR: cannot find or execute $FS_OCTAVE_BIN" > exit 1; > endif > if($?LD_LIBRARY_PATH == 0) setenv LD_LIBRARY_PATH "" > if($#LD_LIBRARY_PATH == 0) then > setenv LD_LIBRARY_PATH $FS_OCTAVE_LIB > else > setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:$FS_OCTAVE_LIB > endif > endif > 470a490 > Probably I am omitting something, but I have no clue what is the problem here :/ Patrycja 2018-07-03 19:35 GMT+02:00 Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>: Are you sure you're using the new one? I've tested it on my system, and it works. On 07/03/2018 01:33 PM, Patrycja Naumczyk wrote: > > External Email - Use Caution > > Douglas, > > thank you for clarifying. The problem is that both when > $FS_MKCON_USE_BIN is not defined and when it is set to '0' mkcontrast2 > asks for MATLAB path (as in my previous mail). What should I do to > make it use octave instead? > > Best regards, > Patrycja > > 2018-07-03 19:23 GMT+02:00 Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>>: > > questions answered below > > On 07/03/2018 01:14 PM, Patrycja Naumczyk wrote: > > > > External Email - Use Caution > > > > Douglas, > > > > thanks a lot - unfortunately this still doesn't work - it stops > at the > > same cause: > > > > mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0 > > INFO: Found 2 Non-Null Conditions > > INFO: Found 3 Delays > > Condition Weights: 1.00000000000000000000 0 > > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh > > -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat > > -wdelay 1 0 0 -octave > > $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ > > cmtxfile PASAT.sm5.lh/test.mat > > nconds 2, wcond 1.00000000000000000000 0 > > ndelays 3, wdelay 1 0 0 > > ndelays 3, wpsa > > sumconds 1 > > sumdelays 0 > > nircorr 0 > > TER 0.050000 > > rdelta > > rtau > > ERROR: cannot find matlab. Is it in your path? > > ERROR running mkcontrast > > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh > > -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat > > -wdelay 1 0 0 -octave > > Tue Jul 3 18:52:59 CEST 2018 > > > > which is apparently when verifying the $FS_MKCON_USE_BIN ? I don't > > have such a variable (I believe it wasn't necessary with v5.3?). > > Looking for it I found that a bunch of environment variables are > > advised in the new FS tutorial > > (http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup <http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup> > <http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup <http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup>>). I > should > > probably update the .bashrc file, but I would like to clarify: > > 1. Are all of variables mentioned below needed for proper v6.0 > FS-Fast > > functioning or are some of them needed only for course settings? > > FS_SPMREG_USE_BIN > > FS_MKCON_USE_BIN > > FS_SXA3_USE_BIN > These are only needed if you want to use the matlabbinaries
> > 2. To use octave instead of MATLAB - only the $FS_MKCON_USE_BIN should > > be set to '0', or should I change any of the other two? > Just FS_MKCON_USE_BIN(or leave it undefined). > > 3. If all three are needed - what do the $FS_SPMREG_USE_BIN and > > $FS_SXA3_USE_BIN stand for? > These are to use the matlab binaries when running these programs > (binaries don't require a license). We do not use spm for > registration > anymore, so that this irrelevant. SXA3 refers to selxavg3-sess. > > 4. Are there any other environment variables that differ between the > > v.5.3 and v6.0 that I should also add? > I don't think so. > > > > Best regards, > > Patrycja > > > > > > > > 2018-07-03 18:31 GMT+02:00 Douglas N. Greve > <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> > > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>>>: > > > > Sorry for the delay. I've put a new version here > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2> > <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2>> > > > <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2> > <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2>>> > > copy it to $FREESURFER_HOME/fsfast/bin > > > > > > > > > > On 07/03/2018 12:13 PM, Patrycja Naumczyk wrote: > > > > > > > > > Hi all, > > > > > > I'll repost - does FSv6 no longer support octave for FS-Fast > > processing? > > > > > > Would appreciate clarification on this :) > > > Patrycja > > > > > > 2018-06-29 21:41 GMT+02:00 Patrycja Naumczyk > > > <patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>> > > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>>> > > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>> > > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>>>>>: > > > > > > Hi all, > > > > > > I just switched from FS 5.3 to 6.0 on Gentoo Linux. > Previously > > > Freesurfer worked fine under octave setup (as > specified here: > > > > > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html
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> > > but after the update, when I tried testing a MATLAB > related > > > function I get an error: > > > > > > mkcontrast-sess -analysis PASAT.sm5.lh -contrast test > -a 1 -c 0 > > > INFO: Found 2 Non-Null Conditions > > > INFO: Found 3 Delays > > > Condition Weights: 1.00000000000000000000 0 > > > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir > > PASAT.sm5.lh > > > -wcond 1.00000000000000000000 0 -sumconds -o > > PASAT.sm5.lh/test.mat > > > -wdelay 1 0 0 -octave > > > $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ > > > cmtxfile PASAT.sm5.lh/test.mat > > > nconds 2, wcond 1.00000000000000000000 0 > > > ndelays 3, wdelay 1 0 0 > > > ndelays 3, wpsa > > > sumconds 1 > > > sumdelays 0 > > > nircorr 0 > > > TER 0.050000 > > > rdelta > > > rtau > > > ERROR: cannot find matlab. Is it in your path? > > > ERROR running mkcontrast > > > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir > > PASAT.sm5.lh > > > -wcond 1.00000000000000000000 0 -sumconds -o > > PASAT.sm5.lh/test.mat > > > -wdelay 1 0 0 -octave > > > Fri Jun 29 21:21:16 CEST 2018 > > > > > > It seems that the environment variable (FS_USE_OCTAVE) is > > > recognized correctly (the function runs with "-octave" > > flag), but > > > somehow is omitted during execution? What can I do > about it? > > > > > > I checked that v.5.3 used mkcontrast, whereas v.6.0 uses > > > mkcontrast2 which does not seem to support octave? Is it > > possible > > > to force calling mkcontrast instead of mkcontrast2? > > > > > > Best regards, > > > Patrycja > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > The information in this e-mail is intended only for the > person to > > whom it is > > addressed. If you believe this e-mail was sent to you in > error and > > the e-mail > > contains patient information, please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>> . If the e-mail was sent > > to you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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Douglas N. Greve -
Patrycja Naumczyk