general-discussion > Sica error
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Nov 30, 2010  07:11 PM | Ricardo Soder
Sica error
Hello all, I am using NIAK, and I have got an error in the sica_subject job, as follow. I would like some help to fix this problem. Thank you

Log of the (matlab) job : sica_subject1_run1
Started on 30-Nov-2010 18:07:32
User: ricsoder
host : pavlov
system : unix

command =


files_in =

fmri: [1x102 char]
mask: [1x77 char]

files_out =

space: [1x113 char]
time: [1x109 char]

opt =

flag_test: 0
folder_out: [1x60 char]
norm: 'mean'
algo: 'Infomax'
nb_comp: 60
flag_verbose: 1

The job starts now !

Spatial independent component analysis
Reading data /home/ricsoder/example/out/intermediate/subject1/time_filter/fmri_subject1_session1_run1_a_mc_f.mnc.gz ...
Reading brain mask /home/ricsoder/example/out/anat/subject1/func_subject1_mask_nativefunc.mnc.gz ...
Correction of the mean of time series ...
Performing spatial independent component analysis with 60 components, this might take a while ...
Reducing the data to 60 principal dimensions...
Data has rank 59. Cannot compute 60 components.

Something went bad ... the job has FAILED !
The last error message occured was :
Error using ==> mtimes
Inner matrix dimensions must agree.
File /home/ricsoder/matlab/niak- at line 175
File /home/ricsoder/matlab/niak- at line 227
File /home/ricsoder/matlab/niak- at line 114

Checking outputs
The output file or directory /home/ricsoder/example/out/quality_control/subject1/corsica/fmri_subject1_session1_run1_a_mc_f_sica_space.mnc.gz has not been generated!
The output file or directory /home/ricsoder/example/out/quality_control/subject1/corsica/fmri_subject1_session1_run1_a_mc_f_sica_time.mat has not been generated!

30-Nov-2010 18:07:37 : The job has FAILED
Total time used to process the job : 5.55 sec.
Nov 30, 2010  07:11 PM | Pierre Bellec
RE: Sica error
Hi Ricardo,

Thanks for posting the first issue on this forum ! What's happening is that the functional data is too small for the number of components you requested. Also, the format of the pipeline has changed slightly with the new release and that may be why the number of components is not fixed correctly. You can check the new syntax in the tutorial :
I made sure the new version is backward compatible, but the trick I used did not work for the parameters of CORSICA. I have created two tickets (102 & 103) on the development website, and these issues will be treated as bugs. See :

In the meantime, please use the following parameter in your script : = 20;

This should solve your problem.

Best regards,

Dec 6, 2010  11:12 AM | Pierre Bellec
RE: Sica error
Dear Ricardo,

Just a quick follow-up. I have solved both issues. The fix will be part of the next release.

Best regards,

Dec 7, 2010  07:12 PM | Pierre Bellec
RE: Sica error
The bug fixes are included in NIAK 0.6.4 that I just released. Good luck with your analysis,