Dear Surfers,
I was running mkcontrast-sess with Matlab and having good success. Then wanted to try Octave for ease of use on a cluster I have access to, and after browsing the listserv set the following:
export FS_USE_OCTAVE=1
export FS_OCTAVE_LIB=/usr/lib64/octave
export FS_OCTAVE_BIN=/usr/bin/octave
However when I run mkcontrast-sess now (on the cluster and a VB ubuntu machine, both without Matlab), it runs through launching Octave and then errors out as noted below. I'm new to using Octave and wasn't sure what else I might need to set up for it to run properly? Any thoughts would be much appreciated.
Best Regards,
Matthew
brain@neurodebian:/usr/local/freesurfer/subjects$ mkcontrast-sess -analysis test.08.lh -contrast faces_gt_objects -a 2 -c 3
INFO: Found 3 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 0 1.00000000000000000000 -1.00000000000000000000 mkcontrast -anadir test.08.lh -wcond 0 1.00000000000000000000 -1.00000000000000000000 -sumconds -o test.08.lh/faces_gt_objects.mat -wdelay 1 -octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile test.08.lh/faces_gt_objects.mat nconds 3, wcond 0 1.00000000000000000000 -1.00000000000000000000 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau GNU Octave, version 3.2.4 Copyright (C) 2009 John W. Eaton and others. This is free software; see the source code for copying conditions. There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. For details, type `warranty'.
Octave was configured for "i486-pc-linux-gnu".
Additional information about Octave is available at http://www.octave.org.
Please contribute if you find this software useful. For more information, visit http://www.octave.org/help-wanted.html
Report bugs to bug@octave.org (but first, please read http://www.octave.org/bugs.html to learn how to write a helpful report).
For information about changes from previous versions, type `news'.
error: `fast_contrastmtx' undefined near line 25 column 21
________________________________
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Hi Matthew, I'm not sure what the issue could be. If you start octave from the command line and type "which fast_contrastmtx" does it say it is not found? doug
On 10/29/12 12:38 PM, Garlinghouse, Matthew wrote:
Dear Surfers,
I was running mkcontrast-sess with Matlab and having good success. Then wanted to try Octave for ease of use on a cluster I have access to, and after browsing the listserv set the following:
export FS_USE_OCTAVE=1
export FS_OCTAVE_LIB=/usr/lib64/octave
export FS_OCTAVE_BIN=/usr/bin/octave
However when I run mkcontrast-sess now (on the cluster and a VB ubuntu machine, both without Matlab), it runs through launching Octave and then errors out as noted below. I'm new to using Octave and wasn't sure what else I might need to set up for it to run properly? Any thoughts would be much appreciated.
Best Regards,
Matthew
*brain@neurodebian:/usr/local/freesurfer/subjects$ mkcontrast-sess -analysis test.08.lh -contrast faces_gt_objects -a 2 -c 3*
**
*INFO: Found 3 Non-Null Conditions*
*INFO: Found 1 Delays*
*Condition Weights: 0 1.00000000000000000000 -1.00000000000000000000*
*mkcontrast -anadir test.08.lh -wcond 0 1.00000000000000000000 -1.00000000000000000000 -sumconds -o test.08.lh/faces_gt_objects.mat -wdelay 1 -octave*
- $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $*
*cmtxfile test.08.lh/faces_gt_objects.mat*
*nconds 3, wcond 0 1.00000000000000000000 -1.00000000000000000000*
*ndelays 1, wdelay 1*
*ndelays 1, wpsa *
*sumconds 1*
*sumdelays 0*
*nircorr 0*
*TER 0.050000*
*rdelta *
*rtau *
*GNU Octave, version 3.2.4*
*Copyright (C) 2009 John W. Eaton and others.*
*This is free software; see the source code for copying conditions.*
*There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or*
*FITNESS FOR A PARTICULAR PURPOSE. For details, type `warranty'.*
**
*Octave was configured for "i486-pc-linux-gnu".*
**
*Additional information about Octave is available at http://www.octave.org.*
**
*Please contribute if you find this software useful.*
*For more information, visit http://www.octave.org/help-wanted.html*
**
*Report bugs to bug@octave.org (but first, please read*
*http://www.octave.org/bugs.html to learn how to write a helpful report).*
**
*For information about changes from previous versions, type `news'.*
**
*error: `fast_contrastmtx' undefined near line 25 column 21*
The Nebraska Medical Center E-mail Confidentiality Disclaimer
The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.
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-
Douglas Greve -
Garlinghouse, Matthew