Documentation/4.2/Modules/TractographyFiducialSeeding - Revision history

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Text replacement - "slicerWiki/index.php" to "wiki"

Alexy at 21:32, 13 August 2013

2013-08-13T21:32:28Z

Alexy at 21:30, 13 August 2013

2013-08-13T21:30:09Z

Alexy at 21:07, 13 August 2013

2013-08-13T21:07:59Z

Alexy at 21:04, 13 August 2013

2013-08-13T21:04:41Z

Alexy at 20:38, 13 August 2013

2013-08-13T20:38:39Z

Alexy at 20:25, 13 August 2013

2013-08-13T20:25:35Z

UpdateBot: Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

2013-06-14T07:42:19Z

Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

UpdateBot: Nightly -> 4.2

2012-10-31T22:01:08Z

Nightly -> 4.2

New page

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Demian Wassermann, SPL 
Contributor1: FIRSTNAME LASTNAME, AFFILIATION 
Contributor2: FIRSTNAME LASTNAME, AFFILIATION 
Contact: Demian Wassermann, <email>demian@bwh.harvard.edu</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:Logo-splnew.jpg|Surgical Planning Laboratory
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
Most frequently used for these scenarios:

* Use Case 1:
* Use Case 2:


{{documentation/{{documentation/version}}/module-section|Tutorials}}
[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial Slicer 4 Diffusion Tensor Tutorial]


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:

{|style="width: 100%"
|
* Input panel1:
** First input
** Second input
* Parameters panel:
** First parameter
** Second parameter
* Output panel:
** First output
** Second output
* Viewing panel:
| align="right" |
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]
|-
|
* Input panel2:
** First input
** Second input
* Parameters panel:
** First parameter
** Second parameter
* Output panel:
** First output
** Second output
* Viewing panel:
| align="right" |
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* Point to other modules that have similar functionality


{{documentation/{{documentation/version}}/module-section|References}}
Publications related to this module go here. Links to pdfs would be useful.
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

@@ Line 9: / Line 9: @@
 {{documentation/{{documentation/version}}/module-introduction-row}}
 This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br>
-Author: Demian Wassermann, SPL<br>
+Author: Alex Yarmarkovich, Isomics, SPL<br>
-Contributor1: FIRSTNAME LASTNAME, AFFILIATION<br>
+Contributor1: Demian Wassermann, SPL<br>
-Contributor2: FIRSTNAME LASTNAME, AFFILIATION<br>
+Contributor2: Steve Pieper, Isomics, SPL<br>
-Contact:  Demian Wassermann, <email>demian@bwh.harvard.edu</email><br>
+Contact:  Alex Yarmarkovich, <email>alexy@bwh.harvard.edu</email><br>
 {{documentation/{{documentation/version}}/module-introduction-row}}
 {{documentation/{{documentation/version}}/module-introduction-logo-gallery

← Older revision		Revision as of 07:42, 14 June 2013
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	{{documentation/{{documentation/version}}/module-header}}		{{documentation/{{documentation/version}}/module-header}}

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 {{documentation/{{documentation/version}}/module-section|Tutorials}}
-[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial Slicer 4 Diffusion Tensor Tutorial]
+[http://wiki.slicer.org/wiki/Documentation/4.0/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial Slicer 4 Diffusion Tensor Tutorial]
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@@ Line 86: / Line 86: @@
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 {{documentation/{{documentation/version}}/module-section|Similar Modules}}
-* Point to other modules that have similar functionality
+* Tractography Label Map Seeding
 <!-- ---------------------------- -->

@@ Line 44: / Line 44: @@
 {|style="width: 100%"
+|
 * Parameters panel:
-** First parameter
+** Parameters: select an existing setting for the module or create a new one.
-** Second parameter
+** Presets: select an Slicer4 or Slicer3 parameters setting for the module.
-* Output panel:
+* IO panel:
-** First output
+** Input DTI volume: select an existing tensor volume.
-** Second output
+** Input FiducialList, Model, or Label Map: select an existing fiducial list, or a model, or a label map volume to be used as seeds for tracking.
-* Viewing panel:
+** Output FiberBundle: Select the bundle that you want to create or modify from a list.
 | align="right" |
 [[Image:Tractography_Fiducial_Seeding.PNG|thumb|280px|Fiducial Tractography Seeding]]
 |-
+|
-* Input panel2:
+* Label Map Options panel:
-** First input
+** Use Index Space: if selected seed at IJK voxel grid
-** Second input
+** Seed Spacing: spacing in between seed points within in the labelmap (in mm), only matters if use Use Index Space is off.
-* Parameters panel:
+** Random Grid: use random placement.
-** First parameter
+** Linear Measure Start Threshold: place seeds only if linear measure (cl) is above this threshold.
-** Second parameter
+** ROI Labels: a comma separated list of label to start seeding
-* Output panel:
+** Write Fibers to Disk: option to save the results to disk for further analysis.
-** First output
+** Output Directory: path where the results are saved.
-** Second output
+** File Prefix Name: name that would be used for each output bundle.
 | align="right" |
 [[Image:Tractography_LabelMap_Seeding.PNG|thumb|280px|Label Map Tractography Seeding]]
 |}
 <!-- ---------------------------- -->

@@ Line 55: / Line 55: @@
 * Viewing panel:
 | align="right" |
-[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]
+[[Image:Tractography_Fiducial_Seeding.PNG|thumb|280px|Name of panel 1]]
 |-
+|

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 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Module Description}}
-Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.
+This module is used for interactive seeding of DTI fiber tracts starting from a list of fiducial points or vertices of a model, or a label map volume.[[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.
@@ Line 29: / Line 29: @@
 Most frequently used for these scenarios:
-* Use Case 1:
+* Use Case 1: Create DTI fiber tracts starting from a list of fiducial points. Tracks created from a small number of fiducial points are are highly interactive and can be used in exploration mode while moving fiducials with the help of transformations. This mode can be useful in pre-op planning or for tracking tools during the surgery.
-* Use Case 2:
+* Use Case 2: Create DTI fiber tracts starting from vertices of a model. This mode can be useful for exploring tracts around a tumor model.
 <!-- ---------------------------- -->