Hello All,

I'm working on setting up NIAK with Singularity on our local Linux server. I am having a problem running niak_pipeline_fmri_preprocess.m

I open the Octave session with Singularity and NIAK loaded using this terminal command: psom_console.sh -p /usr/local/share/singularity/niak-boss-0.17.0.img

When I run the niak_tutorial_fmri_preprocessing command I get the following error message, and this is the same error message I received previously when running niak_pipeline_fmri_preprocess using the files_in and opt arguments just as is done online, but with my own files. Please let me know if you have any ideas for next steps.

Best Regards,
Aki

---Error message for tutorial---
--2017-03-17 18:32:01-- http://www.nitrc.org/frs/download.php/72...
Resolving http://www.nitrc.org (www.nitrc.org)... 132.239.16.23
Connecting to http://www.nitrc.org (www.nitrc.org)|132.239.16.23|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2726269 (2.6M) [application/force-download]
Saving to: '/home/anikolai/SampleData/data_test_niak_mnc1/data_test_niak_mnc1.zip'

100%[===============================================================================================================>] 2,726,269 1.31M/s in 2.0s
2017-03-17 18:32:04 (1.31 MB/s) - '/home/anikolai/SampleData/data_test_niak_mnc1/data_test_niak_mnc1.zip' saved [2726269/2726269]
Deleting file '/home/anikolai/SampleData/data_test_niak_mnc1/data_test_niak_mnc1.zip'
ans = 0
Generating pipeline for individual fMRI preprocessing :
Adding subject1 ; 0.33 sec
Adding subject2 ; 0.33 sec
Adding group-level quality control of coregistration in anatomical space (linear stereotaxic space) ; 0.01 sec
Adding group-level quality control of coregistration in anatomical space (non-linear stereotaxic space) ; 0.01 sec
Adding group-level quality control of coregistration in functional space ; 0.01 sec
Adding group-level quality control of motion correction (motion parameters) ; 0.01 sec
Adding group-level quality control of scrubbing time frames with excessive motion ; 0.00 sec
Adding the report on fMRI preprocessing ; 0.40 sec
Logs will be stored in /home/anikolai/SampleData/fmri_preprocess/logs/
Generating dependencies ...
Percentage completed : 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100- 0.12 sec
Setting up the to-do list ...
I found 75 job(s) to do.
stopped in /usr/local/niak/extensions/psom/psom_run_pipeline.m at line 505
505: [flag_failed,msg] = psom_run_script(cmd_deamon,script_deamon,opt_script,opt_logs);
debug> dbcont
stopped in /usr/local/niak/extensions/psom/psom_run_script.m at line 239
239: if ~isempty(cmd)
debug> dbcont
error: 'gb_psom_opt_matlab' undefined near line 240 column 67
error: called from
psom_run_script at line 240 column 15
psom_run_pipeline at line 505 column 18
niak_pipeline_fmri_preprocess at line 749 column 5
niak_tutorial_fmri_preprocessing at line 75 column 1
error: evaluating argument list element number 3
error: called from
psom_run_script at line 240 column 15
psom_run_pipeline at line 505 column 18
niak_pipeline_fmri_preprocess at line 749 column 5
niak_tutorial_fmri_preprocessing at line 75 column 1
>>

---Error Message on My Files---
pipeline = niak_pipeline_fmri_preprocess(files_in,opt)
warning: The following field(s) were ignored in the structure opt: corsica
warning: called from
psom_struct_defaults at line 112 column 5
niak_pipeline_fmri_preprocess at line 454 column 5
Generating pipeline for individual fMRI preprocessing :
Adding subject1 ; 0.41 sec
Adding subject2 ; 0.39 sec
Adding subject3 ; 0.42 sec
Adding subject4 ; 0.42 sec
Adding group-level quality control of coregistration in anatomical space (linear stereotaxic space) ; 0.01 sec
Adding group-level quality control of coregistration in anatomical space (non-linear stereotaxic space) ; 0.01 sec
Adding group-level quality control of coregistration in functional space ; 0.01 sec
Adding group-level quality control of motion correction (motion parameters) ; 0.01 sec
Adding group-level quality control of scrubbing time frames with excessive motion ; 0.00 sec
Adding the report on fMRI preprocessing ; 0.54 sec

Logs will be stored in /home/anikolai/demo_niak/fmri_preprocess/logs/
Generating dependencies ...
Percentage completed : 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100- 0.31 sec
Setting up the to-do list ...
I found 189 job(s) to do.
error: 'gb_psom_opt_matlab' undefined near line 240 column 67
error: called from
psom_run_script at line 240 column 15
psom_run_pipeline at line 505 column 18
niak_pipeline_fmri_preprocess at line 749 column 5
error: evaluating argument list element number 3
error: called from
psom_run_script at line 240 column 15
psom_run_pipeline at line 505 column 18
niak_pipeline_fmri_preprocess at line 749 column 5