Documentation/Nightly/Extensions/FinslerTractography - Revision history

Alexy at 15:55, 2 May 2014

2014-05-02T15:55:40Z

Alexy at 15:53, 2 May 2014

2014-05-02T15:53:44Z

Alexy at 15:50, 2 May 2014

2014-05-02T15:50:23Z

Alexy at 15:49, 2 May 2014

2014-05-02T15:49:36Z

Alexy at 15:47, 2 May 2014

2014-05-02T15:47:11Z

Alexy at 15:46, 2 May 2014

2014-05-02T15:46:23Z

Alexy: Created page with '{{documentation/versioncheck}} {{documentation/{{documentation/version}}/module-header}}

@@ Line 38: / Line 38: @@
 {{documentation/{{documentation/version}}/extension-section|Tutorials}}
-<gallery widths="200px" perrow="4">
+N/A
 <!-- ---------------------------- -->
@@ Line 53: / Line 46: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-section|References}}
-* G Sharp, N Kandasamy, H Singh, M Folkert, "GPU-based streaming architectures for fast cone-beam CT image reconstruction and demons deformable registration," Physics in Medicine and Biology, 52(19), pp 5771-83, 2007.
+* GJ. Melonakos, E. Pichon, S. Angenent, A. Tannenbaum, 'Finsler Active Contours'. IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3):412-423. March 2008
 <!-- ---------------------------- -->

@@ Line 32: / Line 32: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-section|Use Cases}}
-[http://plastimatch.org/data_sources.html Sample data] to use with modules.
+The Finsler Tractography Module module uses the fast-sweeping algorithm to find the connectivity from a set of seeding points to each voxel in the input DWI volume (or inside the mask, if provided). This connectivity is the minimum cost of arriving at each voxel from the seeds, following the trajectory of the estimated pathways. The cost is computed as the integral along the pathway of a local directional cost computed from the ODF or some other HARDI-related measurement. A complete description of the algorithm may be found in: J. Melonakos, E. Pichon, S. Angenent, A. Tannenbaum, 'Finsler Active Contours'. IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3):412-423. March 2008. A background-removal mask can be used to accelerate computations. Optionally, the algorithm provides at each voxel an estimation of the vector tangent to the optimal pathway at that point (arrival direction). Fast-sweeping is full multi-threaded, and some other accelerations (checking only those voxels in the causal direction of the solution) have been implemented to obtain a result in a reasonable time. However, an algorithm virtually identical to that in the aforementioned paper may be reproduced fixing the advanced parameters as follows: Cost: (E(q)/Phi(r))^3 Directions: 26 Use threads: deactivate Use accelerated iterations: deactivate (Start accelerated iterations becomes irrelevant). <br>
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-section|Tutorials}}

@@ Line 27: / Line 27: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-section|Modules}}
-*[[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography]
+*[[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography Module]]
-*[[Documentation/{{documentation/version}}/Modules/FinslerBacktracing |Backtracing ]]
+*[[Documentation/{{documentation/version}}/Modules/FinslerBacktracing |Backtracing Module]]
 <!-- ---------------------------- -->

@@ Line 27: / Line 27: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-section|Modules}}
-*[[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
+*[[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography]
-*[[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]]
+*[[Documentation/{{documentation/version}}/Modules/FinslerBacktracing |Backtracing ]]
 <!-- ---------------------------- -->

@@ Line 11: / Line 11: @@
 Acknowledgments:
 Supported by grant number FMECD-2010/71131616E from the Spanish Ministry of Education/Fulbright Committee <br>
 Contributors: Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin. The directional iterators were contributed by Luis Ibanez (Kitware).<br>

@@ Line 8: / Line 8: @@
 {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
 {{documentation/{{documentation/version}}/module-introduction-row}}
 Acknowledgments:
-This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by ... <br>
+Supported by grant number FMECD-2010/71131616E from the Spanish Ministry of Education/Fulbright Committee <br>
 Author:Greg Sharp<br>
-Contributors: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}})<br>
+Contributors: Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin. The directional iterators were contributed by Luis Ibanez (Kitware).<br>
-Contact: Greg Sharp, <email>gcsharp@partners.org</email><br>
 {{documentation/{{documentation/version}}/module-introduction-row}}
 {{documentation/{{documentation/version}}/module-introduction-logo-gallery
@@ Line 24: / Line 23: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-section|Extension Description}}
-Plastimatch is an open source software for image computation. Our main focus is high-performance volumetric registration of medical images, such as X-ray computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET). Software features include:
+This module implements the Finsler tractography method with HARDI data described by J. Melonakos et al. From a set of seeding and target points, the paths are estimated as the shortest path taking into account a local, directional dependent cost.
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-section|Modules}}