Introduction

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

Contents of this package

This package provides some tasks and models supporting parts of PSOM.

1. Userfile models

| Name | Description | |------------------|--------------------------------------------------------------------------------------------------------------------------------| | FmriStudy | Superclass of all fMRI study models | | Adhd200FmriStudy | Model for fMRI studies structured according to the conventions used by ADHD | | GobsFmriStudy | Model for fMRI studies structured according to the conventions GOBS | | NiakFmriStudy | Model for fMRI studies structured according to the conventions used by NIAK | | OpenFmriOrgStudy | Model for fMRI studies structured according to the conventions described by OpenfMRI | | XnatFmriStudy | Model for fMRI studies structured according to the conventions described by XNAT |

2. CbrainTasks

| Name | Description | |----------------------------|------------------------------------------------------------------------------------------------| | NiakPipelineFmriPreprocess | A subclass of PsomPipelineLauncher to run NiakPipelineFmriPreprocess | | PsomPipelineLauncher | Generic PSOM pipeline launcher task | | PsomSubtask | Executes a single task inside a PSOM pipeline |

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:

bash cd /path/to/BrainPortal/cbrain_plugins

• Clone this repository. This will create a subdirectory called cbrain-plugins-fmri-psom with the content of this repository:

bash git clone git@github.com:aces/cbrain-plugins-fmri-psom.git

• Run the following rake task:

bash 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):

bash cd /path/to/BrainPortal/cbrain_plugins

• Clone this repository:

bash git clone git@github.com:aces/cbrain-plugins-fmri-psom.git * Run the following rake task (which is not the same as for the BrainPortal side):

bash rake cbrain:plugins:install:plugins

• Restart your execution server (with the interface, click stop, then start).