Modules:ExtractSubvolumeROI-Documentation-3.5 - Revision history

Nicole: /* Source code & documentation */

2010-01-15T23:06:00Z

Source code & documentation

2009-12-21T01:02:36Z

Quick Tour of Features and Use

2009-12-16T14:57:04Z

Development

2009-12-13T20:34:33Z

Development

2009-11-18T17:39:58Z

Quick Tour of Features and Use

2009-11-18T17:34:27Z

Development

2009-11-18T17:33:10Z

Quick Tour of Features and Use

2009-11-18T17:29:20Z

Subvolume extraction with ROI widget

2009-11-16T00:44:49Z

2009-11-16T00:42:04Z

Development

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 Source code can accessed [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/ExtractSubvolumeROI/ here]
-[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.
+[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/ Links] to documentation generated by doxygen.
 == More Information ==

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 ** '''Output volume''' is the volume node where the result of ROI extraction will be stored. Note, that the output volume cannot be identical to the input volume. The module will give you an error if this is the case.
 ** '''Input spacing scaling constant''' is the coefficient used to determine the spacing of the output volume. The output spacing is defined by multiplying the input spacing in each dimension by the user-specified coefficient. For example, if the input spacing is 1x1x1.4, and the scaling coefficient is 0.5, the output volume will have spacing 0.5x0.5x0.7, effectively doubling the resolution of the output image.
 ** '''Interpolation type''' allows to select between Nearest Neighbor, Linear or Cubic interpolators. For subvolumes being extracted from a label volume, you should use Nearest Neighbor interpolator. Otherwise Cubic is the preferred choice. Linear interpolator requires less computation, which may be important for very large ROIs.
 ** '''Do ROI resample''' initiates the subvolume extraction based on the inputs and parameters.

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 * add isotropic resampling mode
 * consider more intuitive in-slice resampling mode; the current one is not quite there when ROI is under transform
 ===Dependencies===

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 Standing issues under development:
 * add isotropic resampling mode
 * consider more intuitive in-slice resampling mode; the current one is not quite there when ROI is under transform

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 * '''Viewing panel:''' The module provides two approaches to change the size and location of the ROI. First, this can be done in 3D View by moving the colored handles of the ROI widget. Second, the ROI can be adjusted in the slice views. ''Right mouse button click'' adjusts the bounds of the ROI. ''Left mouse button click'' moves the center of ROI to be the point where the click was made.
-* The input volume and input ROI are both allowed to be under linear transform. This allows to extract a parallelipiped shaped ROI, which is arbitrarily oriented within the input volume. This can be done by creating a new Transform in the MRML Tree, or in the Transform module, dragging the input ROI under that transform in the MRML Tree, and adjusting the rotation of the ROI from the Transform module.
+* The input volume and input ROI are both allowed to be under linear transform. This allows to extract a parallelepiped shaped ROI, which is arbitrarily oriented within the input volume using these steps:
 Upon completion of the resampling operation, the input volume is set as the Background image volume, and the extracted resampled ROI is set as the Foreground image.

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 Standing issues under development:
-* color map of the output volume is not initialized correctly when operating on label maps
+* color map of the output volume is not initialized correctly when operating on label maps -- DONE
-* ROI overlay image is not aligned with the ROI widget when input volume/ROI are under a transform
+* ROI overlay image is not aligned with the ROI widget when input volume/ROI are under a transform -- DONE
 * Fix Acknowledgements tab to have BSF logo and links to the documentation
 ===Dependencies===

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 {|
+|
 * '''Input/initialization parameters panel:'''
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 * '''Viewing panel:''' The module provides two approaches to change the size and location of the ROI. First, this can be done in 3D View by moving the colored handles of the ROI widget. Second, the ROI can be adjusted in the slice views. ''Right mouse button click'' adjusts the bounds of the ROI. ''Left mouse button click'' moves the center of ROI to be the point where the click was made.
+|

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 |[[Image:extractSubvolume1.png|thumb|280px|Input and initialization of SubvolumeExtractROI]]
 |[[Image:extractSubvolume2.png|thumb|280px|Visualization of the extracted subvolume]]
 |}

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