brainhack-report-formatted.tex

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\dochead{Report from 2015 OHBM Hackathon (HI)}

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\title{Nipype interfaces in CBRAIN}
\vskip2ex
\projectURL{Project URL: \url{http://cbrain.mcgill.ca}}

\author[
addressref={aff1, aff2},
corref={aff1},
email={tristan.glatard@mcgill.ca}
]{\inits{TG} \fnm{Tristan} \snm{Glatard}}
\author[
addressref={aff1},
%
email={samir.das@mcgill.ca}
]{\inits{SD} \fnm{Samir} \snm{Das}}
\author[
addressref={aff1},
%
email={reza.adalat@mcgill.ca}
]{\inits{RA} \fnm{Reza} \snm{Adalat}}
\author[
addressref={aff1},
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email={natacha.beck@mcgill.ca}
]{\inits{NB} \fnm{Natacha} \snm{Beck}}
\author[
addressref={aff1},
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email={remi.bernard@mail.mcgill.ca}
]{\inits{RB} \fnm{Rémi} \snm{Bernard}}
\author[
addressref={aff1},
%
email={najmeh.khalili@mcgill.ca}
]{\inits{NKM} \fnm{Najmeh} \snm{Khalili-Mahani}}
\author[
addressref={aff1},
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email={pierre.rioux@mcgill.ca}
]{\inits{PR} \fnm{Pierre} \snm{Rioux}}
\author[
addressref={aff1},
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email={marc.rousseau@mcgill.ca}
]{\inits{MER} \fnm{Marc-Étienne} \snm{Rousseau}}
\author[
addressref={aff1},
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email={alan.evans@mcgill.ca}
]{\inits{ACE} \fnm{Alan C.} \snm{Evans}}

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\address[id=aff1]{%
  \orgname{McGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for
Neuroinformatics and Mental Health, Montreal Neurological Institute
(MNI), McGill University},
  \city{Montréal},
  \street{3801 University Street, WB-208},
  \postcode{H3A 2B4},
  \postcode{Québec},
  \cny{Canada}
}
\address[id=aff2]{%
  \orgname{University of Lyon, CNRS, INSERM, CREATIS.},
  \city{Villeurbanne},
  \street{7, avenue Jean Capelle},
  \postcode{69621},
  %
  \cny{France}
}

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%\projectURL{\url{http://cbrain.mcgill.ca}}
%\projectURL{http://cbrain.mcgill.ca}

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%{\sffamily\bfseries\fontsize{10}{12}\selectfont Project URL: \url{http://cbrain.mcgill.ca}}

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\section{Introduction}\label{introduction}

We aim at the large-scale, automatic sharing of software tools between
neuroimaging processing platforms, which will increase the relevance of
such platforms by providing them with richer repositories of
higher-quality tools. Currently, efforts are hampered by the repetitive
porting of the same few tools in different platforms. During the HBM
2015 Hackathon, we worked on the export of software tools from the
Nipype workflow engine \cite{Gorgolewski2011} to the CBRAIN web platform
for distributed computing \cite{sherif2014cbrain}. Nipype includes a
large number of tools that would be useful to CBRAIN users.

\section{Approach}\label{approach}

We developed \texttt{nipype2boutiques}, a tool to export Nipype
interfaces to the ``Boutiques'' tool description format (step 1. on
Figure 1.). Boutiques descriptions are importable by CBRAIN and other
platforms (Virtual Imaging Platform \cite{GLAT-13} and the Pegasus
workflow engine \cite{DEEL-16}). They point to a Docker image containing
the implementation of the tool. \texttt{nipype2boutiques} relies on
\texttt{nipype\_cmd}, a tool to run Nipype Interfaces as Linux command
lines. \texttt{nipype2boutiques} parses the inputs and outputs of a
Nipype interface and extracts their name, type, description and position
on the \texttt{nipype\_cmd} command line. \texttt{nipype2boutiques} then
generates a Boutiques descriptor pointing to a Docker image where the
Nipype interface is available. Once a Nipype interface is exported using
\texttt{nipye2boutiques}, it can be imported to CBRAIN.

\begin{figure}[h!]
  \def\svgwidth{\columnwidth}
  \input{architecture.pdf_tex}
  \caption{\label{centfig} System architecture.} 
\end{figure}

\section{Results}\label{results}

We tested \texttt{nipype2boutiques} on a few Nipype interfaces from the
FSL Nipype module. We exported 64 FSL tools automatically from Nipype to
CBRAIN, and made them available at
\url{https://github.com/glatard/boutiques-nipype-fsl}. Limitations
remain on the type of Nipype interface that can be exported by
\texttt{nipype2boutiques}: in particular, InputMultiPath are currently
not supported, and output files have to be written in the execution
directory of the Nipype Interface.

\section{Conclusions}\label{conclusions}

We prototyped a software tool to export Nipype Interfaces as Boutiques
descriptors which can be imported by CBRAIN and other platforms.
Although the solution is still limited to simple interfaces, we believe
that it has the potential to enable fully-automatic tool sharing between
Nipype and CBRAIN. Future extensions of \texttt{nipype2boutiques} will
be published in the Nipype Github repository at
\url{https://github.com/nipy/nipype}. We also plan on a tighter
integration of Nipype workflows in CBRAIN, following the model adopted
in \cite{GLAT-16}.

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\begin{backmatter}

\section*{Availability of Supporting Data}
More information about this project can be found at: \url{http://cbrain.mcgill.ca}. Further data and files supporting this project are hosted in the \emph{GigaScience} repository REFXXX.

\section*{Competing interests}
None

\section*{Author's contributions}
TG wrote the software and the report; SD contributed to the concept
elaboration at the OHBM event, RA, NB, PR and MER provided support on
the CBRAIN framework, RB implemented Boutiques in CBRAIN, NKM provided
background information on fMRI packages, ACE spearheaded the project.

\section*{Acknowledgements}
The authors would like to thank the organizers and attendees of the 2015
OHBM Hackathon.

  
  
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