Dear Lea,
you should definitely update to a newer version, because this is already solved in newer versions.
Best,
Christian
On Wed, 27 Nov 2019 16:34:43 +0000, Lea Michel <[log in to unmask]> wrote:
>Hello,
>I'm running a surface-based-morphometry analysis on cat12 (version r1059 (2016-10-28)) with SPM12 on Matlab R2015b. I tried to run the segmentation by splitting job into separate processes like it’s suggested on the BATCH but the analysis kept crashing (error 1) and from what I understood I guess it’s not happy to write several reports at the same time.
>So as it was advised in another message from the SPM list (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1705&L=SPM&D=0&P=267332) I tried to stop it from showing the report but still save it by using the shell script cat_batch_spm.sh with the help of other researchers.
>I launched the Matlab cluster from the terminal, then I launched the SPM from Matlab. Then I inserted pathdef in the BATCH file just before the matlabbatch command. And I typed this command in the terminal: /usr/local/spm_toolboxes/cat12/cat_batch_spm.sh BATCH_segmentation_697.m -m /usr/local/bin/matlab2015b_cluster
>So, first the shell script, then my Batch and the matlab command.
>Then I got the error 2, it seems that the paths to SPM are not defined when MATLAB executes the Batch file even with the addition of the pathdef commands. Do you have any ideas of how I could solve this issue or a different idea to enable the the analysis to be split in separate processes ?
>Thank you in advance
>
>Best,
>Léa Michel
>
>ERROR 1
>Quality check: 10s
>
>------------------------------------------------------------------------
>CAT Preprocessing error: MATLAB:class:InvalidHandle: ./02-0172/structural/TD_M_02-0172_T1.nii,1
>------------------------------------------------------------------------
>Invalid or deleted object.
>------------------------------------------------------------------------
> 300 - spm_figure
> 2109 - cat_main
> 614 - cat_run_job
> 13 - cat_run_newcatch
> 247 - run_job
> 155 - cat_run
>------------------------------------------------------------------------
>Developer display mode!
>
>Print 'Graphics' figure to:
> /projects/buic212/T1_Structural_Scans_MASTER_FILE/Lea/T1-Structural_Scans_SBM/02-0132/structural/report/catreport_020132_T1.pdf
>{Error using fill3
>Vectors must be the same length.
>
>Error in cat_io_report (line 418)
> fill3(haxis(1),hdata{1}(1,:),hdata{1}(2,:),hdata{1}(3,:),hdata{1}(4,:)/
> xlims{1}(2)*size(cmap,1)*WMfactor,'EdgeColor','r');
>
>Error in cat_run_newcatch (line 63)
> cat_io_report(job,qa)
>
>Error in cat_run>run_job (line 247)
> cat_run_newcatch(job,tpm,subj);
>
>Error in cat_run (line 155)
>varargout{1} = run_job(job);
>}
>
>
>ERROR 2:
>
>----------------------------------
>Thu Nov 14 13:00:20 GMT 2019
>----------------------------------
>
>/usr/local/spm_toolboxes/cat12/cat_batch_spm.sh BATCH_segmentation_697_test
>
>
> < M A T L A B (R) >
> Copyright 1984-2015 The MathWorks, Inc.
> R2015b (8.6.0.267246) 64-bit (glnxa64)
> August 20, 2015
>
>
>To get started, type one of these: helpwin, helpdesk, or demo.
>For product information, visit www.mathworks.com.
>
>
> Academic License
>
>{ Undefined function or variable 'spm_get_defaults'.
>
>Error in cat_batch_spm (line 11)
>spm_get_defaults;
>}
>com.mathworks.util.ShutdownRuntimeException: Java is shutting down
> at com.mathworks.services.Prefs.nativeGetPreferencesDirectory(Native Method)
> at com.mathworks.services.Prefs.getPropertyDirectory(Prefs.java:198)
> at com.mathworks.services.binding.MatlabKeyBindingPreferenceUtils.resolveToPrefDir(MatlabKeyBindingPreferenceUtils.java:112)
> at com.mathworks.services.binding.MatlabKeyBindingPreferences.getModifiedDefaultFile(MatlabKeyBindingPreferences.java:213)
> at com.mathworks.services.binding.MatlabKeyBindingPreferences.resolveModifiedDefaultFilesFromPrefs(MatlabKeyBindingPreferences.java:116)
> at com.mathworks.services.binding.MatlabKeyBindings.initializeFromPrefs(MatlabKeyBindings.java:717)
> at com.mathworks.services.binding.MatlabKeyBindings.<clinit>(MatlabKeyBindings.java:590)
> at com.mathworks.widgets.debug.DebuggerManager$ActionShell.<init>(DebuggerManager.java:194)
> at com.mathworks.widgets.debug.DebuggerManager$ActionShell.<init>(DebuggerManager.java:190)
> at com.mathworks.widgets.debug.DebuggerManager$DebuggerShellActions$1.<init>(DebuggerManager.java:97)
> at com.mathworks.widgets.debug.DebuggerManager$DebuggerShellActions.<clinit>(DebuggerManager.java:97)
> at com.mathworks.widgets.debug.DebuggerManager.getContinueAction(DebuggerManager.java:292)
> at com.mathworks.matlabserver.worker.service.breakpoint.impl13b.DebuggerInstaller.<init>(DebuggerInstaller.java:46)
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
> at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
> at java.lang.reflect.Constructor.newInstance(Unknown Source)
> at java.lang.Class.newInstance(Unknown Source)
> at com.mathworks.matlabserver.a.b.R(Unknown Source)
> at com.mathworks.matlabserver.a.b.<init>(Unknown Source)
> at com.mathworks.matlabserver.a.b.<init>(Unknown Source)
> at com.mathworks.matlabserver.a.f.initialized(Unknown Source)
> at com.mathworks.matlabserver.connectorcommon.b.b.run(Unknown Source)
> at com.mathworks.matlabserver.connectorcommon.util.g.run(Unknown Source)
> at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
> at java.util.concurrent.FutureTask.run(Unknown Source)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
> at java.lang.Thread.run(Unknown Source)
>
>
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