Funding: Made possible by U24 EB028980 award from NIH/NIBIB

Script & direction: Louisa Bokacheva, PhD

Video editing: ReAgency

Resolution: Best viewed at 1080p on FireVoxel Tutorials YouTube channel

  1. Basic operations. Load and view images in DICOM and other formats, obtain image information, and save images as FireVoxel documents and in Analyze and NIFTI formats.
  2. View options. Adjust grayscale window, select color maps, use zoom tools, view images in different projections and customize user interface.
  3. Raster ROIs. Create image layers, draw and edit raster ROIs, use Fill and Morph tools for faster ROI editing, obtain ROI statistics, save ROIs.
  4. Vector ROIs (VROIs). Create, move and resize VROIs; adjust properties; extend 2D VROI in 3D and 4D; measure distance; save and load VROIs; image crop.
  5. Advanced Raster ROIs. Use ROI operations to segment tissues; threshold to ROI; Peel operation; maximal connected component; connected component by seed; Grow operation; compare ROIs; estimate segmentation accuracy.
  6. Introduction to EdgeWave Segmentation. Introduce EdgeWave tool for automatic segmentation; illustrate the internal steps of EdgeWave using basic ROI and layer operations to segment fat tissues (total fat, subcutaneous fat, and visceral fat); then use EdgeWave for the same task.
  7. Introduction to MRI Non-uniformity Correction. Introduce MRI non-uniformity artifacts; overview of N3 and N4 algorithms; perform N3 and N4 non-uniformity correction; introduce BiCal algorithm; use BiCal to perform non-uniformity correction.
  8. Introduction to MagTrace Tools for Semi-Automatic Segmentation. Introduce MagTrace tools for semi-automatic segmentation; customize MagTrace parameters; draw MagTrace vector contours and rasterize them; use MagTrace to segment organs and tissues.
  9. Introduction to Dynamic Modeling. Load 4D documents; view and save time-activity curves; manipulate 3D and 4D ROIs; perform voxel- and ROI-based 4D processing; generate parametric maps.
  10. Image-Derived Input Function (IDIF). Describe the IDIF algorithm; explain the IDIF tool’s parameters; demonstrate the use of the IDIF tool in DCE MRI in the abdomen and prostate and dynamic PiB PET in the brain.
  11. Image Transformations. Perform interactive image translation and rotation; change voxel size (subsampling, oversampling); reformat.
  12. Coregistration Based on DICOM Tags. Coregister two 3D DICOM images acquired within the same session using orientation and position attributes.
  13. Coregistration Using Mutual Information. Coregister two 3D images using mutual information; demonstrate coregistration of MR and CT images.