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General

 

The batchtool was created out of the needs to apply common neuroimaging pipelines (like SPM, FSL, Freesurfer) on medium sized projects (10-1000 subjects) in a convenient and efficient manner. One of the major objective of NORA's batchtool is to deal with heterogenous data. Typically files (a.k.a. image series) are selected by file patterns, which can iteratively generalized. Errors can be easily tracked by a simple error logging system. For example, it is simple to select a errornous subgroup and rerun a modified job for them, which was corrected for the error. Processing pipelines (batches) are a simple linear series of jobs. Depending on the dependenciesrelationship between theindividual jobs, they can run serially or in parallel. 

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In conclusion, what it provides:

  • Convenient selection of subject/study sets to apply certain processing pipelines
  • Definitions of inputs via Tags or filepatterns with wildcards
  • Composition of processing pipelines based on predefined scripts/jobs (mostly MATLAB), or custom MATLAB/BASH/Python code
  • Submission of jobs to a cluster (Slurm/SGE) with direct access to logs and errors

 

Batchtool

The subject/studies table on the left is used for the selection of subject/studies on which you want to run your batch.  You can use the filter bars to create the subgroup you want to work on (see Subject/Studies table). 

 

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