Difference between revisions of "Modules:Volumes-Documentation"

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  [[Documentation|Return to Slicer Documentation]]
 
  [[Documentation|Return to Slicer Documentation]]
  
[[Image:VolumesModule.png|thumb|350px|right|overview]]
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[[Image:VolumesModule.jpg|right|overview]]
 
* The Volumes Module loads, saves and adjusts display parameters of volume data.
 
* The Volumes Module loads, saves and adjusts display parameters of volume data.
  
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** select the volume that you want to load
 
** select the volume that you want to load
 
** If needed edit the name that will be displayed for this volume inside slicer
 
** If needed edit the name that will be displayed for this volume inside slicer
** If your volume is not a nrrd or dicom format, try loading with "centered" selected instead of from file.
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** 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
 
** 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!'''
 
** Active Volume: determines which volume is manipulated by the Display section. '''Make sure that you select the Volume that you intend to work on!'''
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** Window/Level can be set manually or automatically.
 
** 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.
 
** Threshold is a way to make the background black disappear in the 3D view, when slices are turned to visible.
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** '''pressing the shift key''' allows fine control while adjusting the sliders
 
** For labelmaps you can select here the proper look-up table through the Color Select pull-down.
 
** 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 select a component of the volume to visualize.
** For DWI volumes you can edit the gradient directions usind the Gradient Editor described below.
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** 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 tenosr volume (such as FA) to visualize.
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** 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.
 
** For DTI volumes you can control the tensor glyphs visualization on the slice planes using the Glyph On Slices Display editor described below.
* DWI Gradient Editor
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* [[Modules:Volumes:Diffusion_Editor-Documentation| Diffusion Editor]]
** Will be described by Kerstin
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** For DWI
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*** editing gradients manually or load existing gradients from file (.txt or .nhdr).
 +
*** editing the measurement frame manually or simply rotate/swap/negate columns by selecting them.
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*** testing the parameters by estimating a tensor and displaying glyphs and tracts.
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** For DTI
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*** editing the measurement frame as described above. 
 +
*** testing by displaying glyphs and tracts.
 
* Glyph On Slices Display editor
 
* Glyph On Slices Display editor
 
** Controls the tensor glyphs visibility on individual slices in both 3D and 2D viewers.
 
** Controls the tensor glyphs visibility on individual slices in both 3D and 2D viewers.

Latest revision as of 13:43, 8 June 2008

Home < Modules:Volumes-Documentation
Return to Slicer Documentation
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.
    • pressing the shift key allows fine control while adjusting the sliders
    • 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
      • editing gradients manually or load existing gradients from file (.txt or .nhdr).
      • editing the measurement frame manually or simply rotate/swap/negate columns by selecting them.
      • testing the parameters by estimating a tensor and displaying glyphs and tracts.
    • For DTI
      • editing the measurement frame as described above.
      • testing by 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)