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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 tasks and models supporting parts of the MNI tools.

NOTE: Many of these MNI tools are not yet available publicly (CIVET for instance) so installing this package is of little utility for most installations.

1. Userfile models

Name Description
CivetOutput Model for CIVET outputs
CivetStudy Model for several outputs of CIVET
DicomCollection Model for a collection of DICOM files
DicomFile Model for DICOM file
FunctionalNiftiFile Model for functional NIfTI medical data files
LorisSubject Model for LORIS subject files
MgzFile Model for MGZ structural files
Minc1File Model for MINC files in MINC1 format
Minc2File Model for MINC files in MINC2 format
MincCollection Model for a collection of MINC files
MincFile Model for MINC files; superclass of MINC1 and MINC2
NiftiFile Model for NIfTI medical data files
StructuralNiftiFile Model for structural NIfTI medical data files

2. CbrainTasks

Name Description
Civet To run CIVET pipeline
CivetCombiner Combines several CivetOutputs into a single CivetStudy
CivetQc To run CIVET QC pipeline on a CivetStudy
Dcm2mnc To run dcm2mnc, in order to convert DICOM to MINC
Dcm2nii To run dcm2nii, in order to convert DICOM to NIfTI
MincConvert To run minc_convert, in order to convert MINC1 to MINC2 or MINC2 to MINC1
Mnc2nii To run mnc2nii, in order to convert MINC to NIfTI
Nii2mnc To run nii2mnc, in order to convert NIfTI to MINC
NuCorrect To run nu_correct

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-mni with the content of this repository:
git clone [email protected]:aces/cbrain-plugins-mni.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-mni.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).