BrainSuite in Nipype: Interactive Tutorial

Estimated time to complete: 1 hour (+6 hours of processing time)

We have developed an interactive tutorial that executes Cortical Surface Extraction, BDP, SVReg, and thicknessPVC in a parallel processing Nipype workflow. Our interactive tutorial is presented through Jupyter Notebooks.

You may view our tutorial page here, without the need to install any dependencies; however you will not be able to execute any code.

A non-interactive version of our tutorial can be viewed at the bottom of this page, or can be viewed here, without the need to install any dependencies. Continue reading to use our interactive tutorial.

Installing dependencies

  1. If you haven’t already done so, follow the installation instructions provided on our Nipype Installation page.
  2. Install Jupyter Notebook. Follow the instructions on Jupyter’s Installation page

Acquiring our Jupyter Notebook tutorial

Our Jupyter Notebook file can be downloaded manually here, or can be acquired through the following bash commands:

curl http://users.bmap.ucla.edu/~jwong/BrainSuiteNipypeParallel.ipynb -o “BrainSuiteNipypeParallel.ipynb”

Running the interactive tutorial

  1. From the terminal, cd to wherever you saved our Jupyter Notebook file
  2. Run the following command. A browser with an active Jupyter Notebook session will start up shortly
    jupyter notebook
  3. From the Jupyter Notebook session in your browser, open the file:
    [Nipype Tutorial] Cortical Surface Extraction, BDP, SVReg, in Parallel
  4. Read the introduction in the tutorial, and begin our tutorial.

View our tutorial below (non-interactive)