/AABA_23_SlicerMorph

The SlicerMorph workshop for the AABA 2023

Due to the uncertainty of the on-site WIFI quality, please install the software and download the sample dataset prior to workshop. Please bring a laptop and a mouse for the workshop.

Download and install 3D Slicer and the SlicerMorph Extension

1. Download and install the stable release (v5.2.2) of 3D Slicer based on your computer's operating system (Windows, Mac, or Linux) here: https://download.slicer.org

2. Install the SlicerMorph Extension for 3D Slicer (you can also follow the instruction in the "Installation" session here: https://github.com/SlicerMorph/SlicerMorph#installation).

  • Open 3D Slicer and click "Extension Wizard" from the top bar. In the Extension Wizard window, click "Install Extension", and then search for "SlicerMorph". Click "Install". It may take a minute. After that, click "Restart Slicer" to finish installation. It may take a minute.

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  • Click "Restart" at the lower right corner of the Extension Wizard to finish the Installation.

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  • You should able to see the SlicerMorph extension installed in the "Manage Extensions" of the Extension Wizard.

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Download sample data

For this workshop, we are going to use the CT image series of a human head from MorphoSource as the sample data. Download the sample data here: https://www.morphosource.org/concern/media/000367572?locale=en. You will need to create a MorphoSource account. Unzip the file. Open the unzipped folder, in the folder "Media 000367572 - Head Ct CTImageSeries CT", you should see another zipped folder "tif-000367572" that contains the TIFF series. Unzip this folder as well.

Topics will be covered in the workshop

  • 3D Slicer and SlicerMorph overview and utilities
  • 3D volumetric data visualization, and segmentation
  • Landmark annotation and automated landmarking
  • SlicerMorph and geometric morphometrics
  • Load SlicerMorph landmark coordinates into R

Pre/Post Workshop Self-Help pointers

  1. 3D Slicer User Manual
  2. SlicerMorph Github Repository: contains install instructions, papers to cite for functionality, and links to module documentation.
  3. SlicerMorph Tutorials Repository: contains step-by-step instructions for each SlicerMorph module and some of the core Slicer modules (e.g., segment editor)
  4. SlicerMorph Youtube channel: contains video tutorials. For some videos, the UI may look slightly different depending on the version of Slicer used at the time
  5. 3D Slicer Community Forum: To ask questions that you couldn't find answers to in links above
  6. Consider sign up to the SlicerMorph mailing list to keep up-to-date with SlicerMorph project and extension updates
  7. Monthly SlicerMorph office hours: 4th Tuesday of every month at 11 (Seattle Time). Please sign up to the mailing list above for the meeting Zoom link.
  8. Follow the SlicerMorph team's Twitter!
  9. Follow my Twitter!