https://github.com/aces/cbrain-plugins-freesurfer
(Deprecated) FreeSurfer models and tasks for CBRAIN
Science Score: 10.0%
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(Deprecated) FreeSurfer models and tasks for CBRAIN
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Metadata Files
README.md
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_pluginsdirectory under BrainPortal:
bash
cd /path/to/BrainPortal/cbrain_plugins
- Clone this repository. This will create a subdirectory called
cbrain-plugins-freesurferwith the content of this repository:
bash
git clone git@github.com:aces/cbrain-plugins-freesurfer.git
- Run the following rake task:
bash
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_pluginsdirectory under BrainPortal (yes, BrainPortal, because that's where files are installed; on the Bourreau sidecbrain_pluginsis a symbolic link):
bash
cd /path/to/BrainPortal/cbrain_plugins
- Clone this repository:
bash
git clone git@github.com:aces/cbrain-plugins-freesurfer.git
* Run the following rake task (which is not the same as for
the BrainPortal side):
bash
rake cbrain:plugins:install:plugins
- Restart your execution server (with the interface, click stop, then start).
Owner
- Name: ACElab
- Login: aces
- Kind: organization
- Location: Montreal, Quebec, Canada
- Website: http://mcin.ca/
- Repositories: 75
- Profile: https://github.com/aces
McGill Centre for Integrative Neuroscience (MCIN) - Alan C. Evans, Ph.D., Principal Investigator
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