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Introduction

This repository is a package containing a set of plugins for the CBRAIN platform.

Contents of this package

This package provides some support models, tasks and data providers for interacting with LORIS installations.

1. Userfile models

Name Description
LorisBySubjectAndVisit A FileCollection used to represent the mappings in LorisPhantomNativeSshDataProvider

2. CbrainTasks

Name Description
TODO TODO

3. DataProviders

All these DataProviders ruby models implement subclasses of the SshDataProvider, where the target files are selectively chosen among the directory structure for the LORIS Assembly file system tree.

Name Description
LorisAssemblyNativeSshDataProvider Maps only MINC files in */*/mri/native/*.mnc
LorisAssemblyProcessedSshDataProvider Maps any files in */*/mri/processed/*
LorisCcnaPhantomAssemblyNativeSshDataProvider Like LorisAssemblyNativeSshDataProvider except the path components are more strictly controlled
LorisPhantomNativeSshDataProvider Maps Loris repository according to some convention regarding the Subject_id and the Visit_id

How to install this package

An existing CBRAIN installation is assumed to be operational before proceeding.

This package must be installed once on the BrainPortal side of a CBRAIN installation, and once more on each Bourreau side.

1. Installation on the BrainPortal side:

  • Go to the cbrain_plugins directory under BrainPortal:
cd /path/to/BrainPortal/cbrain_plugins
  • Clone this repository. This will create a subdirectory called cbrain-plugins-neuro with the content of this repository:
git clone git@github.com:aces/cbrain-plugins-loris.git
  • Run the following rake task:
rake cbrain:plugins:install:all
  • Restart all the instances of your BrainPortal Rails application.

2. Installation on the Bourreau side:

Note: If you are using the Bourreau that is installed just besides your BrainPortal application, you do not need to make any other installation steps, as they share the content of the directory cbrain_plugins through a symbolic link; you only need to restart your Bourreau server.

  • Go to the cbrain_plugins directory under BrainPortal (yes, BrainPortal, because that's where files are installed; on the Bourreau side cbrain_plugins is a symbolic link):
cd /path/to/BrainPortal/cbrain_plugins
  • Clone this repository:
git clone git@github.com:aces/cbrain-plugins-loris.git
  • Run the following rake task (which is not the same as for the BrainPortal side):
rake cbrain:plugins:install:plugins
  • Restart your execution server (with the interface, click stop, then start).

3. In case of problems during installation

  • Consider running the rake task that cleans all previous installations of tools and userfiles, then trying again the rake tasks mentioned above.
rake cbrain:plugins:clean:all