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:

• parts of the FreeSurfer suite.
• parts of the FMRIB Software Library (FSL).
• parts of the MNI tools.

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 git@github.com: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 git@github.com: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