/SVP_2022

SVP 2022 Digital Morphology and Shape Analysis with SlicerMorph

Prior to workshop

We are not sure about the WIFI quality at the conference, so we advise getting the software and the sample dataset prior to workshop on 1st.

Download the stable version (v5.0.3) of the Slicer for your computer

How to install SlicerMorph Extension for 3D Slicer

Download link for sample data:

This share contains three files:

  1. Hypertrag_UW13933Slices.zip: Original image stack courtesy of Anne Kort. This is the original data format provided by the imaging center. This is a massive dataset (uncompressed 32GB) and when unzipped has 3754 TIFF files. The image spacing is 0.0346mm (or 34.6 micron). If you wanto import this dataset at its original resolution, you will need a computer with minimum of 48GB (64GB is better) RAM. We will show you how you use ImageStacks module of SlicerMorph to effectively import this data into 3D Slicer.
  2. preview.nrrd: This is the same dataset above imported at preview resolution of original dataset (each axis is reduced by 4, so resolution is now 0.1384mm) and saved in NRRD format. This dataset can be directly loaded into Slicer. If you have a computer that has 8GB RAM (or less), please only use this dataset.
  3. half_resolution.nrrd: This is the same dataset above imported at half resolution of original dataset (each axis is reduced by 2, so resolution is now 0.0692mm) and saved in NRRD format. This dataset can be directly loaded into Slicer. If you have a computer that has 16GB RAM (or more), you can use this dataset.

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 signign up to the SlicerMorph announcement 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 for the meeting link.
  8. Consider using SlicerMorphCloud platform to process large dataset: Apply for an account here -ORCID is required