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-freesurfer.
This repository is a package containing a set of plugins for the CBRAIN platform.
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.
| 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 |
| 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 |
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.
- Go to the
cbrain_pluginsdirectory under BrainPortal:
cd /path/to/BrainPortal/cbrain_plugins- Clone this repository. This will create a subdirectory called
cbrain-plugins-mniwith the content of this repository:
git clone git@github.com:aces/cbrain-plugins-mni.git- Run the following rake task:
rake cbrain:plugins:install:all- Restart all the instances of your BrainPortal Rails application.
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_pluginsdirectory under BrainPortal (yes, BrainPortal, because that's where files are installed; on the Bourreau sidecbrain_pluginsis a symbolic link):
cd /path/to/BrainPortal/cbrain_plugins- Clone this repository:
git clone git@github.com: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).