Modules:Volumes-Documentation

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overview

• The Volumes Module loads, saves and adjusts display parameters of volume data.

• Load
  • select the volume that you want to load
  • If needed edit the name that will be displayed for this volume inside slicer
  • If your volume is not a nrrd or dicom format, select "centered" for image origin, else select "from file".
  • If this is a label map, click the box
  • Active Volume: determines which volume is manipulated by the Display section. Make sure that you select the Volume that you intend to work on!

• Display
  • Allows you to adjust the way that a volume is displayed
  • Window/Level can be set manually or automatically.
  • Threshold is a way to make the background black disappear in the 3D view, when slices are turned to visible.
  • For labelmaps you can select here the proper look-up table through the Color Select pull-down.
  • For DWI volumes you can select a component of the volume to visualize.
  • For DWI volumes you can edit the gradient directions and measurement frame using the Diffusion Editor described below.
  • For DTI volumes you can select a scalar drived component of the tensor volume (such as FA) to visualize.
  • For DTI volumes you can control the tensor glyphs visualization on the slice planes using the Glyph On Slices Display editor described below.
• Diffusion Editor
  • For DWI
    • you can edit gradients manually or load existing gradients from file (.txt or .nhdr).
    • you can edit the measurement frame manually or simply rotate/swap/negate columns by selecting them.
    • you can do some testing with the parameters by estimating a tensor and displaying glyphs and tracts.
  • For DTI
    • you can edit the measurement frame as described above.
    • you can do some testing with displaying glyphs and tracts.
• Glyph On Slices Display editor
  • Controls the tensor glyphs visibility on individual slices in both 3D and 2D viewers.
  • Selects the scalar to color the glyphs by and the color map to apply.
  • Controls glyphs opacity, glyph type, scale and sampling rate.
• Info
  • Provides some basic information about the Volume

• Save
  • Lets you save a volume. Make sure to provide an extension (such as myvolume.nrrd)