general-discussion > psom_run_script- no gb_psom_opt_matlab
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Mar 17, 2017  01:03 PM | Aki Nikolaidis
psom_run_script- no gb_psom_opt_matlab
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
Mar 21, 2017  08:03 PM | Pierre Bellec
RE: psom_run_script- no gb_psom_opt_matlab
Hi Aki,

Sorry for the late answer. Could you please give it a try with the new 0.18.1 release?
https://hub.docker.com/r/simexp/niak-bos...

Best,

Pierre
Mar 24, 2017  12:03 PM | Aki Nikolaidis
RE: psom_run_script- no gb_psom_opt_matlab
Hi Pierre,

My apologies, I'm a little unclear on what do download and what to do with it. We are running NIAK on Singularity instead of Docker, would there be a Singularity .img file you can point me to for the 0.18.1 release?

best regards,
Aki
Apr 14, 2017  09:04 AM | Pierre Bellec
RE: psom_run_script- no gb_psom_opt_matlab
Hi Aki,

I believe soon you will be able to pull directly images from docker hub using singularity. In the meantime we are releasing the images on github, as binaries: 
https://github.com/SIMEXP/niak/releases

Check the link to niak-boss-0.18.1.img.gz

Best,

Pierre
Apr 14, 2017  10:04 AM | Aki Nikolaidis
RE: psom_run_script- no gb_psom_opt_matlab
Hi Pierre,

Thanks! We were able to convert the docker image to singularity and run it successfully on our local server.

Thanks for the help!

Best,
Aki
Apr 27, 2017  08:04 PM | Pierre Bellec
RE: psom_run_script- no gb_psom_opt_matlab
Very happy to hear that! 

Best,

Pierre