Modules:Volumes-Documentation-3.4 - Revision history

Nicole: /* Source code & documentation */

2010-01-15T21:30:33Z

Source code & documentation

Marianna at 19:53, 26 May 2009

2009-05-26T19:53:19Z

Fedorov: /* Source code & documentation */

2009-02-19T14:12:32Z

Source code & documentation

Alexy at 21:48, 11 February 2009

2009-02-11T21:48:32Z

Alexy: New page: Return to Slicer 3.4 Documentation NOTOC ===Module Name=== '''Volumes''' overview == General Information == ===Module Type & Ca...

2009-02-11T21:47:47Z

New page: Return to Slicer 3.4 Documentation __NOTOC__ ===Module Name=== '''Volumes''' right|overview == General Information == ===Module Type & Ca...

New page

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Module Name===
'''Volumes'''
[[Image:VolumesModule.jpg|right|overview]]

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Alex Yarmarkovich, Isomics, SPL
* Contact: Alex Yarmarkovich, alexy@bwh.harvard.edu

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

== Usage ==
* 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.
* [[Modules:Volumes:Diffusion_Editor-Documentation-3.4| 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)

===Examples, Use Cases & Tutorials===

*Tutorial about [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training loading and viewing data].

===Quick Tour of Features and Use===

* '''Load:''' Load volumes into Slicer3
* '''Display:''' Adjust volume display parameters
* '''Infol:''' General information about volume
* '''Save:''' Saves volume onto disk

== Development ==

===Dependencies===

Other modules or packages that are required for this module's use.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Follow this [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/ link] to the ChangeTracker source code in ViewVC.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classes.html Documentation] generated by doxygen.

== More Information ==

===Acknowledgment===

===References===

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 Follow this [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/ link] to the Volumes source code in ViewVC.
-[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classes.html Documentation] generated by doxygen.
+[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html Documentation] generated by doxygen.
 == More Information ==

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