general-discussion > Error in NIAK Preprocessing in SICA with QSUB
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Oct 10, 2013  07:10 AM | Sulantha Sanjeewa
Error in NIAK Preprocessing in SICA with QSUB
Hi,
I use QSUB for NIAK preprocessing. When I run the jobs, some jobs fail in the SICA job with the following error.
I also tried with skipping SICA with setting the skip sica flag  = 1 , but still I get this error and fail the jobs. Thank you for your support.

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Log of the (matlab) job : sica_subject4237_run2
Started on 09-Oct-2013 11:20:22
User: sulantha
host : broca
system : unix
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The job starts now !
********************
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Spatial independent component analysis
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Warning: The RandStream.setDefaultStream static method will be removed in a
future release.  Use RandStream.setGlobalStream instead.
> In RandStream.RandStream>RandStream.setDefaultStream at 456
In psom_set_rand_seed at 79
In niak_brick_sica at 189
In psom_run_job>sub_eval at 214
In psom_run_job at 128
Reading data /home/sulantha/NIAKOutput/preprocessing/intermediate/subject4237/regress_confounds//fmri_subject4237_session2_run1_cor.mnc ...
Reading brain mask /home/sulantha/NIAKOutput/preprocessing/anat/subject4237/func_subject4237_mask_stereonl.mnc ...
Correction of the mean of time series ...
Performing spatial independent component analysis with 60 components, this might take a while ...
********************
Something went bad ... the job has FAILED !
The last error message occured was :
Error using inv
Too many output arguments.
File /home/sulantha/niak/commands/sica/niak_sica.m at line 943
File /home/sulantha/niak/commands/sica/niak_sica.m at line 183
File /home/sulantha/niak/bricks/sica/niak_brick_sica.m at line 238
File /home/sulantha/niak/extensions/psom-1.0.2/psom_run_job.m at line 214
File /home/sulantha/niak/extensions/psom-1.0.2/psom_run_job.m at line 128
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Checking outputs
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The output file or directory /home/sulantha/NIAKOutput/preprocessing/quality_control/subject4237/corsica/fmri_subject4237_session2_run1_cor_sica_space.mnc has not been generated!
The output file or directory /home/sulantha/NIAKOutput/preprocessing/quality_control/subject4237/corsica/fmri_subject4237_session2_run1_cor_sica_time.mat has not been generated!
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09-Oct-2013 11:20:31 : The job has FAILED
Total time used to process the job : 9.21 sec.
**********************************************
ans =
1
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OUTPUT QSUB
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ERROR QSUB
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No window system found.  Java option 'MWT' ignored.
Oct 23, 2013  12:10 AM | Pierre Bellec
RE: Error in NIAK Preprocessing in SICA with QSUB
Dear Sulantha,

Sorry for the delay in response. I somehow missed this email. There seems to be an issue with a call to the function "inv". This function does return two outputs, but here it complains it has only one. My first guess is that you have a function called "inv" that supersede the regular matlab/octave command. Try to type:

which int

If this points to a function in your own libraries, that's the problem. All you need to do then is to make sure that when you run a NIAK pipeline, only NIAK is loaded in the matlab/octave search path. You may also want to consider renaming this function to avoid future trouble. 

If that's not the problem, please provide the version number of octave or matlab, as well as the system that you use. 

I hope this helps. Best regards,

Pierre