Monday, September 15, 2014

Connectome Workbench: 1st Steps

Here's my advice for getting started with the Connectome Workbench:
  1. First, go through my tutorial on getting started with Workbench: it describes downloading Workbench, starting it, loading images, and viewing overlay and underlay images.
  2. This tutorial introduces wb_command, and shows how to use it to create a surface file from a volumetric NIfTI (for quick-viewing purposes, not for further analysis).
  3. Read my summary of the different file types.
  4. Try the official Workbench tutorial (or at least look through the manual to get an idea of the possibilities).
  5. Look at my post on using the Workbench with volumetric images.
And why bother learning Workbench? Setting aside all its surface and CCF/HCP functionality (and that's a lot to set aside), I think the ability to create "scenes" justifies the time spent learning the software.

This screenshot shows scenes in action: clicking the little button marked with yellow arrows brings up the scene dialog box. I have three scenes stored in this file, and selecting one for display changes Workbench to recreate exactly how it was when the scene was created: window size, colors and scaling, loaded images, tab layout. Creating scenes for each image that might be used in a publication can save massive amounts of time: need to adjust a threshold or change a color? Just bring up the scene and make the change, no need to start from the beginning.

 UPDATE 26 March 2020: linked to the new getting-started tutorial.
UPDATE 8 February 2018: linked to the new volume to surface tutorial; fixed the official tutorial link.
UPDATE 2 August 2017: removed the (very outdated!) mention of the release of Connectome Workbench 1.0; renamed this post to the more general "Connectome Workbench: 1st Steps".

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