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 the FMRIB Software Library (FSL).

Important Note : Because this package required the NiftiFile userfile model, you must also install the MNI plugin package for CBRAIN. This can be done separately, before or after this package is installed.

1. Userfile models

Name	Description
FslDesignFile	Model for FSL design file
FslFastOutput	Model for FAST output
FslFirstOutput	Model for FIRST output
FslMelodicOutput	Model for MELODIC output

2. CbrainTasks

Name	Description
FslBedpostx	To run BEDPOSTX
FslBet	To run BET
FslFast	To run FAST
FslFeat	To run FEAT
FslFirst	To run FIRST
FslFlirt	To run FLIRT
FslMelodic	To run MELODIC
FslProbtrackx	To run PROBTRACKX

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.

Important : The prerequisite MNI plugin package for CBRAIN must also be installed.

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-fsl with the content of this repository:

git clone [email protected]:aces/cbrain-plugins-fsl.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 [email protected]:aces/cbrain-plugins-fsl.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).