Mindboggle 2016

Introduction

Mindboggle’s open source brain morphometry platform takes in preprocessed T1-weighted MRI data, and outputs volume, surface, and tabular data containing label, feature, and shape information for further analysis. Mindboggle can be run on the command line as “mindboggle”. The program is written in Python 3 and Python-wrapped C++ code called within a Nipype pipeline framework.

Installed version(s)

This version is installed and currently available on environment hpc-env/6.4:

Mindboggle/1.2.4-foss-2017b-Python-3.6.3
Mindboggle/1.3.4-foss-2017b-Python-3.6.3

Using Mindboggle

If you want to find out more about Mindboggle on the HPC Cluster, you can use the command

module spider Mindboggle

This will show you basic informations e.g. a short description and the currently installed version.

To load the desired version of the module, use the command, e.g.

module load hpc-env/6.4 
module load Mindboggle

Always remember: this command is case sensitive!

Besides Mindboggle itself, the module also loads various dependencies, which can all be used separately. Some of the dependencies are:

• ANTs
• MESA
• FreeSurfer
• HDF5
• ...

To list every single loaded dependency, type in the following after loading the Mindboggle module:

module list

Documentation

The full documentation can be found here. More information about the first commands and a short tutorial can be found here.