Modules:EMDTIClustering-Documentation-3.6 - Revision history

Mmaddah: /* Module Name */

2010-12-18T00:32:58Z

Module Name

Mmaddah: /* Module Name */

2010-12-18T00:31:50Z

Module Name

Mmaddah: /* Authors, Collaborators & Contact */

2010-05-10T18:58:48Z

Authors, Collaborators & Contact

Mmaddah at 14:45, 4 May 2010

2010-05-04T14:45:56Z

Mmaddah: /* Acknowledgment */

2010-04-28T19:06:57Z

Acknowledgment

Mmaddah: /* Tests */

2010-04-28T19:06:21Z

Tests

Mmaddah: /* Development */

2010-04-14T15:35:19Z

Development

Mmaddah at 14:42, 14 April 2010

2010-04-14T14:42:13Z

Mmaddah: Created page with 'Return to Slicer 3.5 Documentation Gallery of New Features NOTOC ===Module Name=== EM Fiber Clustering Module …'

2010-04-14T14:41:51Z

Created page with 'Return to Slicer 3.5 Documentation Gallery of New Features __NOTOC__ ===Module Name=== EM Fiber Clustering Module …'

New page

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

[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
EM Fiber Clustering Module

{|
|[[File:shot1.png|thumb|280px|Module interface]]
|[[File:shot2.png|thumb|280px|Trajectories colored by their cluster ID]]
|}

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

Type: CLI

Category: Clustering

===Authors, Collaborators & Contact===
* Mahnaz Maddah
* James Miller
* Contact: Mahnaz Maddah, maddah@ge.com

===Module Description===

This module clusters a set of input trajectories into a number of bundles, generates arc length parameterization by establishing the point correspondences and reports diffusion parameters along the bundles as well as the membership probability of each trajectory in each cluster. The module requires specification of seed trajectories (or initial centerlines) as representatives of the desired bundles.

== Usage ==

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

Tutorial and test data can be downloaded from here:

http://www.nitrc.org/projects/quantitativedti/

===Quick Tour of Features and Use===
Here is a list of the panels in the module:

* '''IO panel:'''
''Trajectories'' Input trajectories to be clustered.
''Output Clusters'' Clustered trajecories labeled by their cluster ID.
''Initial Centers'' [optional] Initial center(s). Note that intial centers need
to be provided by passing either a set of trajectories here or a fiducial list.
''Fiducials to Pick Initial Centers'' [optional] A fiducial list to generate initial center(s). For each fiducial
in the list the closest trajectory in the input is selected as the initial center.
''Output Initial Centers'' [Optional] Selected initial cluster centers.
''Output Final Centers'' [Optional] Final cluster centers, colored by the mean FA value along the bundle
if "Perform Quantitative Analysis" is flaged .
''Perform Quantitative Analysis'' Flag that needs to be marked if quantitative analysis is desired to be done.
''Output Directory'' A directory needs to be specified if performing quantitative analysis.
''File Prefix Name'' Prefix of the output files generated through tract-oriented analysis.
''[[CSVfilesDescription|Description of generated CSV files by EM Clustering Module]]''

* '''Clustering Parameters:'''
''Compactness of Fiber Bundles'' Parameter between 1 and 5 that specifies the extent of similarity between the
trajectories of each cluster. Increase the value for more compact bundles.

* '''Advanced Parameters:'''
''Space Resolution'' Space resolution for distance map calculation.
''Iterations'' Maximum number of EM iterations.
''Maximum Distance'' Maximum distance in mm specifies an upper threshold on the distance of points that
can contribute to new center formation.

== Development ==

===Dependencies===

===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===

Source code [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti link]

== More Information ==

===Acknowledgment===

===References===

[http://www.slicer.org/publications/pages/display?search=mahnaz+maddah&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked Publications]

← Older revision		Revision as of 00:32, 18 December 2010
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−	'''For version 3.6.2 and beyond, please refer to [[EM DTI Fiber Clustering Module-Documentation-3.6.2]].''' The new version has two new capabilities: Atlas-based seeding and multi-subject tract-based quantitative analysis.	+	'''For version 3.6.2 and beyond, please refer to [[DTI Fiber Clustering Module-Documentation-3.6.2]].''' The new version has two new capabilities: Atlas-based seeding and multi-subject tract-based quantitative analysis.

	== General Information ==		== General Information ==

@@ Line 1: / Line 1: @@
 [[Documentation-3.6|Return to Slicer 3.6 Documentation]]
-[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]
+[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]
 __NOTOC__

@@ Line 80: / Line 80: @@
 On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:
-* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
+* Test [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/QuantitativeDiffusionTools/trunk/EMClustering/?root=quantitativedti EMClusteringTest.cxx]
 ===Known bugs===

← Older revision		Revision as of 14:42, 14 April 2010
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−	[[Documentation-3.5\|Return to Slicer 3.5 Documentation]]	+	[[Documentation-3.6\|Return to Slicer 3.6 Documentation]]

	[[Announcements:Slicer3.5#Highlights\|Gallery of New Features]]		[[Announcements:Slicer3.5#Highlights\|Gallery of New Features]]

@@ Line 11: / Line 11: @@
 |[[File:shot2.png|thumb|280px|Trajectories colored by their cluster ID]]
 |}
 == General Information ==

@@ Line 22: / Line 22: @@
 * Mahnaz Maddah
 * James Miller
-* Contact: Mahnaz Maddah, maddah@ge.com
+* Contact: Mahnaz Maddah, mmaddah [at] alum.mit.edu
 ===Module Description===

@@ Line 97: / Line 97: @@
 ===Acknowledgment===
 ===References===
 [http://www.slicer.org/publications/pages/display?search=mahnaz+maddah&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked Publications]

@@ Line 66: / Line 66: @@
 == Development ==
 ===Dependencies===
 ===Known bugs===

Modules:EMDTIClustering-Documentation-3.6 - Revision history

Mmaddah: /* Module Name */

Mmaddah: /* Module Name */

Mmaddah: /* Authors, Collaborators & Contact */

Mmaddah at 14:45, 4 May 2010

Mmaddah: /* Acknowledgment */

Mmaddah: /* Tests */

Mmaddah: /* Development */

Mmaddah at 14:42, 14 April 2010

Mmaddah: Created page with 'Return to Slicer 3.5 Documentation Gallery of New Features __NOTOC__ ===Module Name=== EM Fiber Clustering Module …'

Mmaddah: Created page with 'Return to Slicer 3.5 Documentation Gallery of New Features NOTOC ===Module Name=== EM Fiber Clustering Module …'