Modules:ROISelect-Documentation-3.6 - Revision history

Grundlett: Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

2019-11-27T02:33:38Z

Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

Alexy: /* Quick Tour of Features and Use */

2010-07-02T19:46:01Z

Quick Tour of Features and Use

Alexy: /* Module Description */

2010-07-02T19:42:09Z

Module Description

Lauren at 18:48, 8 April 2010

2010-04-08T18:48:09Z

Lauren: Created page with 'Return to Slicer 3.5 Documentation NOTOC ===Module Name=== ROI Select {| |Before |} {| |…'

2010-04-08T18:47:01Z

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[[Documentation-3.5|Return to Slicer 3.5 Documentation]]

__NOTOC__
===Module Name===
ROI Select

{|
|[[Image:SlicerImage_roi_select_tract_before.png|thumb|280px|Before]]
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|[[Image:SlicerImage_roi_select_tract_after.png|thumb|280px|After]]
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== General Information ==
===Module Type & Category===

Type: CLI

Category: Tractography -> Editor

===Authors, Collaborators & Contact===
* Author1: Lauren O'Donnell, BWH
* Contributor1: Alex Yarmakovich, Isomics
* Contact: http://lmi.bwh.harvard.edu/~odonnell]

===Module Description===
ROI Select allows a user to select tracts passing through a region of interest (ROI). The ROI is defined as a labelmap and has to be provided by the user. One approach to generate the ROI is by means of the Editor module.

== Usage ==

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

We want to select only those tracts passing through a given region, where that region is defined using a labelmap. This can be used to get a more thorough seeding by seeding in a large region and selecting a subset of tracts that are of interest (as opposed to seeding directly in the region of interest). Additionally, ROIs can be used to "clean up" seeding from fiducials by retaining only those fibers of interest.

*First, a region of interest in the tract that is under study has to be defined for each subject, for example by manually delineating the ROI using the Editor module. The Fractional Anisotropy (FA) Volume can be used as reference volume to trace the ROI. The FA volume can be computed using [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 Diffusion Tensor Scalar Measurements].
*Second, if the DTI volume is not direcly available, the DWI has to be loaded and the tensor has to be created using the [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.4 | Diffusion Tensor Estimation].
*Third, seed tractography either using ROI Seeding (normally with a larger or different region than selection ROI) or Fiducial Seeding using the DTI volume.
*Fourth, select fibers of interest using ROI Select.

===Quick Tour of Features and Use===
The module is very straighforward to use:

* '''Input ROI A:'''set the labelmap volume that is going to be used for selection
* '''ROI definition panel:'''
* '''ROI pass label:'''set the label value that is going to be used for fiber selection (AND)
* '''ROI not pass label:''' (optional) set the label value that is going to be used for fiber rejection (NOT)
* '''Output panel:'''
* '''Viewing panel:'''

=== Caveats and other limitations ===
ROISelect module may not work when there are transforms applied to the ROI labelmap or fiber tracts in the scene.

== Development ==

===Dependencies===

None

===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===

Information about the DTMRI infrastructure in Slicer 3 and related classes can be found [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI here]

[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

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@@ Line 34: / Line 34: @@
 We want to select only those tracts passing through a given region, where that region is defined using a labelmap. This can be used to get a more thorough seeding by seeding in a large region and selecting a subset of tracts that are of interest (as opposed to seeding directly in the region of interest). Additionally, ROIs can be used to "clean up" seeding from fiducials by retaining only those fibers of interest.
-*First, a region of interest in the tract that is under study has to be defined for each subject, for example by manually delineating the ROI using the Editor module. The Fractional Anisotropy (FA) Volume can be used as reference volume to trace the ROI. The FA volume can be computed using [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 Diffusion Tensor Scalar Measurements].
+*First, a region of interest in the tract that is under study has to be defined for each subject, for example by manually delineating the ROI using the Editor module. The Fractional Anisotropy (FA) Volume can be used as reference volume to trace the ROI. The FA volume can be computed using [[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4|Diffusion Tensor Scalar Measurements]].
-*Second, if the DTI volume is not direcly available, the DWI has to be loaded and the tensor has to be created using the [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.4 | Diffusion Tensor Estimation].
+*Second, if the DTI volume is not direcly available, the DWI has to be loaded and the tensor has to be created using the [[Modules:DiffusionTensorEstimation-Documentation-3.4|| Diffusion Tensor Estimation]].
 *Third, seed tractography either using ROI Seeding (normally with a larger or different region than selection ROI) or Fiducial Seeding using the DTI volume.
 *Fourth, select fibers of interest using ROI Select.
@@ Line 69: / Line 69: @@
 ===Source code & documentation===
-Information about the DTMRI infrastructure in Slicer 3 and related classes can be found [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI here]
+Information about the DTMRI infrastructure in Slicer 3 and related classes can be found [[Slicer3:DTMRI|here]]
 [http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/ Links] to documentation generated by doxygen.

@@ Line 44: / Line 44: @@
 * '''Input ROI A:'''set the labelmap volume that is going to be used for selection
 * '''ROI definition panel:'''
-* '''ROI pass label:'''set the label value that is going to be used for fiber selection (AND)
+* '''ROI pass label:'''set the label value(s) that is going to be used for fiber selection (AND). A comma separated list of label values of ROI labels that defines pass region. The fiber will pass through all labels.
-* '''ROI not pass label:''' (optional) set the label value that is going to be used for fiber rejection (NOT)
+* '''ROI not pass label:''' (optional) set the label value(s) that is going to be used for fiber rejection (NOT). A comma separated list of label values of ROI labels that defines no pass region.
 * '''Output panel:'''
 * '''Viewing panel:'''