DEPRECATED

The content of this package is deprecated; please use the combined package cbrain-plugins-neuro instead, which include the code here as well as the plugins in cbrain-plugins-fsl and cbrain-plugins-mni.

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 FreeSurfer suite.

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
ReconAllCrossSectionalOutput	Model for recon-all cross sectional output, result of the first step in longitudinal studies
ReconAllBaseOutput	Model for recon-all unbiased base output, result of the second step in longitudinal studies
ReconAllLongiOutput	Model for recon-all longitudinal output, result of the third step in longitudinal studies
ReconAllOutput	Model for recon-all collection (not directly used). All the ReconAll*Output inherits this model

2. CbrainTasks

Name	Description
ReconAll	To run recon-all
ReconAllLongi	To run Longitudinal Stream

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-freesurfer with the content of this repository:

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