Niak Hack

How to do a Niak release

Niak has its releasing utilities inside the util/ directory Here is how to use it

Debugging NIAK Pipelines

First check for failed jobs in the logs folder:

path_logs = '/data/logs/';
psom_pipeline_visu(path_logs,'failed')

Change directory to the logs folder and load the pipeline jobs:

cd(path_logs)
pipe = load('PIPE_jobs');

Then select the failed job:

  job = pipe.<failed_job_name>;

Look for the function that generated the error:

job.command

Search for the function path then open it in a script editor (ex: vim):

which <function_name>
vim   <function_path_name>

figure out which line in function is problematic then put stop point :

  dbstop('<function_name>',<line_number>);

Run the job, and it will start the debugging mode after stopping in the breakpoints you already set:

  psom_run_job (job)

Find problems in a comparison test

When running niak_test, to check if csv files have outputs different than 1.0000 or 0.0000

/>$ grep -nE  ",[0-1]\.0*[1-9]+" *.csv

Visualize outputs of the GLM-connectome pipeline

Using MRIcron in the command line. All commands need to run from the result folder scixx_scgxx_scfxx/<test_name>

• To visualize the percentage of discovery :

  mricron ~/database/template.nii.gz -c -0 -o perc_disc*.nii* -c 5redyell -l 0.01 -h 0.3 -z &
  mricron ~/database/white_template.nii.gz -c -0 -o perc_disc*.nii* -c 5redyell -l 0.01 -h 0.3 -z &

• To visualize the partition :

  mricron ~/database/template.nii.gz -c -0 -o ../networks*.nii* -c NIH -l 0.9 -h 16 -z &
  mricron ~/database/white_template.nii.gz -c -0 -o ../networks*.nii* -c NIH -l 0.9 -h 16 -z &

• To visualize a t-test map, with FDR threshold and range from 0.01 to 5 (hot), combined with range from -5 to -0.01 (winter):

  mricron ~/database/template.nii.gz -c -0 -o fdr_*.nii.gz -c 5redyell -l 0.01 -h 5 -z -o fdr_*.nii* -c 2winter -l -5 -h -0.01 &
  mricron ~/database/white_template.nii.gz -c -0 -o fdr_*.nii.gz -c 5redyell -l 0.01 -h 5 -z -o fdr_*.nii* -c 2winter -l -5 -h -0.01 &

• To visualize a t-test map, without FDR threshold and range from 0.01 to 5 (hot), combined with range from -5 to -0.01 (winter):

  mricron ~/database/template.nii.gz -c -0 -o ttest_*.nii.gz -c 5redyell -l 2 -h 5 -z -o ttest_*.nii* -c 2winter -l -5 -h -2 &
  mricron ~/database/white_template.nii.gz -c -0 -o ttest_*.nii.gz -c 5redyell -l 2 -h 5 -z -o ttest_*.nii* -c 2winter -l -5 -h -2 &