Documentation/4.2/Modules/Volumes

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For the latest Slicer documentation, visit the 4.8 page.


Introduction and Acknowledgements


Information on NA-MIC can be obtained from the NA-MIC website.
Author: Steve Pieper, Isomics, Inc.
Contributor1: Nicole Aucoin, SPL
Contributor2: Alex Yarmarkovich, Isomics, Inc.
Contributor3: Julien Finet, Kitware, Inc.
Contact: Steve Pieper,

Isomics, Inc.  
Kitware, Inc.  
National Alliance for Medical Image Computing (NA-MIC)  
Surgical Planning Laboratory (SPL)  

Module Description

This module is used for changing the appearance of various volume types.


Use Cases

  1. Examples:
    1. Use the SampleData module to load the MR Head volume. You can control the scalar display options using this module.
    2. Use the SampleData module to download the DTI Head volume. A tensor-specific display interface will allow you to display a variety of scalar modes and display glyphs.
  2. When loading a 2D image(jpg, png, tiff ...), the window level(colors) might be skewed. To see the original colors switch the Window Level combobox to Manual Min/Max, then set Min to 0 and Max to 255.
    1. Also use the Spacing field to enter the volumetric pixel sizes of the image data.
    2. While you can display color volumes as slices, most slicer modules do not work natively with RGB or RGBA data, the new VectorToScalarVolume converter can be used to create a volume for use, for example, with the Editor. (added post-4.1).

Tutorials

Panels and their use

Parameters:
  • Active Volume
  • Volume Information
    • Image Dimensions: The number of pixels in "IJK" space - this is the way the data is arranged in memory. The IJK indices (displayed in the DataProbe) go from 0 to dimension-1 in each direction.
    • Image Spacing: The physical distance between pixel centers when mapped to patient space expressed in millimeters.
    • Image Origin: The location of the center of the 0,0,0 (IJK) pixel expressed with respect to patient space. Patient space is organized with respect to the subject's Right, Anterior, and Superior anatomical directions. See http://www.slicer.org/slicerWiki/index.php/Coordinate_systems for more information.
    • Center Volume: This button will adjust the Image Origin so that the entire volume is centered around 0,0,0 in patient space.
    • Scan Order: Describes the image orientation (how the IJK space is oriented with respect to patient RAS.
    • Number of Scalars: Most CT or MR scans have one scalar component (grayscale). Color images have three components (red, green, blue). Tensor images have 9 components. For diffusion weighted volumes this indicates the number of baseline and gradient volumes.
    • Scalars Type: Tells the computer representation of each pixel. Most operations work independent of scalar type. Label map volumes must be of type Short for use with the Editor module.
    • Filename: Path to the file which this volume was loaded from/saved to
    • LabelMap: Indicates and controls if the Volume is a label map
    • Window/Level Presets: Loaded from DICOM headers defined by scanner or by technician.
  • Display
    • Lookup Table: Select the color mapping for scalar volumes to colors.
    • Interpolate: When checked, slice views will display linearly interpolated slices through input volumes. Unchecked indicates nearest neighbor resampling
    • Window Level Presets: Predefinied shortcuts to window/level and color table combinations for common visualization requirements.
    • Window/Level Controls: Double slider with text input to define the range of input volume data that should be mapped to the display grayscale. Auto window level tries to estimate the intensity range of the foreground image data.
    • Threshold: Controls the range of the image that should be considered transparent when used in the foreground layer of the slice display. Same parameters also control transparency of slice models displayed in the 3D viewers.
    • Histogram: Shows the number of pixels (y axis) vs the image intensity (x axis) over a background of the current window/level and threshold mapping.
  • Diffusion Weighted Volumes
    • DWI Component: Selects the baseline or diffusion gradient direction volume to display.
  • Diffusion Tensor Volumes
    • Scalar Mode: Mapping from tensor to scalar.
    • Glyphs on Slices Display: Allows display of graphics visualizations of tensors on one or more of the standard Red, Green, or Yellow slice views.
    • Opacity: How much of the underlying image shows through the glyphs.
    • Scalar Color Map: How scalar measures of tensor are mapped to color.
    • Color by Scalar: Which scalar metric is used to determine the color of the glyphs.
    • Scalar Range: Defines the min-max range of the scalar mapping to color. When enabled, allows a consistent color mapping independent of the full range of the currently displayed item (if not selected color range will cover min-max of the currently displayed data).
    • Glyph Type: Tubes and line show direction of eigen vector of tensor (major, middle, or minimum as selected by the Glyph Eigenvector parameter). Ellipsoid shows direction and relative scale of all three eigenvectors.
    • Scale Factor: Controls size of glyphs. There are no physical units for this parameter.
    • Spacing: Controls the number of glyphs on the slice view.
    • Glyph Eigenvector: Selects which aspect of tensor controls orientation of glyphs.
VolumesModule-2011-11-25.png
On mouse over, a second popup appears under the window level double slider. Large dynamic range can be controlled using the slider. Moving the handles of the popup double slider changes the whole range of the window level double slider.

Similar Modules

  • Each displayable type has a similar visualization control interface (for example, the Models, Tractography, Annotations...).

References

N/A

Information for Developers


IO

Here is the list of supported file formats.

Important classes:

qSlicerVolumesIO.[h/cxx]]
vtkSlicerVolumesLogic.[h/cxx]
vtkSlicerArchetypeVolumesStorageNode.[h/cxx]

The following options can be passed to load volumes programmatically:

Option Type Default Description
labelmap bool false Mark the volume a label map
center bool false Discard file origin information and move the center of the volume in 0,0,0
singleFile bool false Load the file as part of a series of 2D files that represent a 3D volume
autoWindowLevel bool true Automatically compute the window level based on the volume pixel intensities
discardOrientation bool false Discard file orientation information