Nipype 2016

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Nipype, an open-source, community-developed initiative under the umbrella of NiPy, is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL, FreeSurfer, AFNI, Slicer, ANTS), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems.

Nipype allows you to:

  • easily interact with tools from different software packages
  • combine processing steps from different software packages
  • develop new workflows faster by reusing common steps from old ones
  • process data faster by running it in parallel on many cores/machines
  • make your research easily reproducible
  • share your processing workflows with the community 1

Installed version(s)

The following versions are installed and currently available...

... on environment hpc-env/8.3:

  • Nipype/1.7.0-foss-2019b-Python-3.7.4

Loading Nipype

To load the desired version of the module, use the module load command, e.g.

module load hpc-env/8.3
module load Nipype

Always remember: this commands are case sensitive!

Using Nipype

The Nipype installation provides multiple binary files to use. After loading the module, the following executables can be called indepededly from your current directory:

  • csv2rdf
  • nipypecli
  • prov-compare
  • prov-convert
  • rdf2dot
  • rdfgraphisomorphism
  • rdfpipe
  • rdfs2dot

To find out on how to use Nipype, most of the binaries have a help function. e.g. you can just type in nipypecli --help after loading the module to print out a help text to get you started:

$ nipypecli  --help
Usage: nipypecli [OPTIONS] COMMAND [ARGS]...

  -h, --help  Show this message and exit.

  convert  Export nipype interfaces to other formats.
  crash    Display Nipype crash files.
  run      Run a Nipype Interface.
  search   Search for tracebacks content.
  show     Print the content of Nipype node .pklz file.
  version  Print current version of Nipype.


The full documentation can be found at the GitHub page.