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Introduction

This repository is a package containing a set of plugins for the CBRAIN platform. This repository supersedes the content of three other packages: cbrain-plugins-freesurfer, cbrain-plugins-fsl and cbrain-plugins-mni.

Contents of this package

This package provides some tasks and models supporting:

1. Userfile models

For Freesurfer tools:

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
MghFile Model for MGH structural files

For FSL tools:

Name Description
FslDesignFile Model for FSL design file
FslDesignCollection Model for FSL collection with matrix for FSL randomise
FslFastOutput Model for FAST output
FslFirstOutput Model for FIRST output
FslMelodicOutput Model for MELODIC output
NiftiFile Model for NIfTI medical data files
StructuralNiftiFile Model for structural NIfTI medical data files
FunctionalNiftiFile Model for functional NIfTI medical data files

For MNI and DICOM tools:

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 a DICOM file
LorisSubject Model for LORIS subject 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

For BIDS:

Name Description
BidsDataset Model for BIDS dataset

2. CbrainTasks

For Freesurfer tools:

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

For FSL tools:

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
FslRandomise To run RANDOMISE
FslAnat To run FSL-ANAT
ICA-AROMA To run ICA-AROMA

For MNI and DICOM tools:

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
MincBet To run brain extraction tool wrapper

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 [email protected]:aces/cbrain-plugins-neuro.git
  • Run the following rake task:
rake cbrain:plugins:install:all
  • The BIDS dataset viewer requires the bids-validator command-line tool to be installed on the portal host:
  1. Install nodejs
  2. Install bids-validator:
npm install -g  bids-validator
  • 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-neuro.git
  • Run the following rake task (which is not the same as for the BrainPortal side):
rake cbrain:plugins:install:plugins
  • If you want FSL tools to be parallelized in CBRAIN (limited to FSL Melodic for now), replace the fsl_sub script in your FSL installation with the one in the plugin:
cp cbrain-plugins-neuro/bin/fsl_sub ${FSLDIR}/bin
  • 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