general-discussion > niak without Corsica gives an error
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Dec 2, 2010  08:12 AM | Cecile Madjar
niak without Corsica gives an error
Hi -

there is an error occurring when trying to run Niak preprocessing pipeline without Corsica correction of physiological noise.

#######################################################################################
#### if this option is given
opt.corsica.flag_skip = 1; % Skip CORSICA (0: do not skip, 1 : skip)

#### this error occur while launching the pipeline
Generating pipeline for individual fMRI preprocessing :
subject1 ; error: `session' undefined near line 350 column 53
error: called from:
error: /svn/niak/trunk/pipeline/niak_pipeline_corsica.m at line 350, column 41
error: /svn/niak/trunk/pipeline/niak_pipeline_fmri_preprocess_ind.m at line 659, column 38
error: /svn/niak/trunk/pipeline/niak_pipeline_fmri_preprocess.m at line 409, column 18
error: /database/RSCO2/niak/fmri_preprocess_2dec2010/niak_fmri_preprocess_2dec2010.m at line 155, column 17

### => /database/RSCO2/niak/fmri_preprocess_2dec2010/niak_fmri_preprocess_2dec2010.m is the script called to launch niak preprocessing pipeline
the line 155 of this script is
[pipeline,opt] = niak_pipeline_fmri_preprocess(files_in,opt);

#######################################################################################
#### if this option is given
opt.corsica.flag_skip = 0; % Skip CORSICA (0: do not skip, 1 : skip)

### everything runs smoothly

Thanks for your help solving this issue!

C├ęcile
Dec 2, 2010  11:12 AM | Pierre Bellec
RE: niak without Corsica gives an error
Dear Cecile,

Tanks a lot for reporting that bug. I think I fixed it. You can try it out on the development version installed on peuplier. Please let me know if things ran smoothly. This fix will be included in the stable release due soon.

Best regards,

Pierre