UpdateBot: Nightly -> 4.10

2018-10-19T00:44:51Z

Nightly -> 4.10

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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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'''''Extensions:''''' ShapeRegressionExtension 
'''''Author:''''' Laura Pascal (Kitware Inc.) 
'''''Contributors:''''' Beatriz Paniagua (Kitware Inc), James Fishbaugh (University of North Carolina) 
'''''Contact:''''' Laura Pascal, <email>laura.pascal@kitware.com</email>, Beatriz Paniagua, <email>beatriz.paniagua@kitware.com </email> 
'''''Acknowledgments:''''' NIH NIBIB R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects) 
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]

<gallery class="center">
Image:Kitware-logo.png|Kitware Inc.
Image:UofM-logo.png|University of Michigan
</gallery>

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{{documentation/{{documentation/version}}/module-section|Extension Description}}


This extension is composed by two modules :
* RegressionComputation:
** Computation of time-regressed shapes in a collection of 3D shape inputs associated to a linear variable thanks to [https://github.com/laurapascal/shape4D shape4D] CLI.
* RegressionVisualization:
** Plotting of the time-regressed shape volume evolution according to a linear variable
** Visualization of the sequence of the time-regressed shapes generated (using [[Documentation/{{documentation/version}}/Extensions/Sequences|Sequences]] module)


{{documentation/{{documentation/version}}/module-section|Interface}}

Regression Computation module:

[[Image:RegressionComputation-Interface.png|550px|thumb|center]]

Regression Visualization module:

[[Image:RegressionVisualization-Interface.png|550px|thumb|center]]



{{documentation/{{documentation/version}}/module-section|Use Cases}}

==Regression Computation Module==
This module is a user-friendly interface allowing to easily use [https://github.com/laurapascal/shape4D shape4D] CLI in order to compute time-regressed shapes in a collection of 3D shape inputs associated to a linear variable.

===Shape4D Inputs===

{|
|[[Image:RegressionComputation-InputShapeParameters.png|thumb|500px|Regression Computation Input Shape Parameters]]
|This section allows the user to specify the input shapes for each time point as well as their associated parameters.
To do so, the user can either specify :
* A folder containing the input shapes. The user would then have to specify the parameters associated to each input shape. A CSV file (''CSVInputshapeparameters.csv'') containing all these information will be automatically created in the output folder specified by the user.
* A CSV files containing in each row the input shape file path followed by the shape parameters "Time Point" , "Sigma W" , "Tris" and "Weight" .
[[Image:RegressionComputation-ExampleInputShapeParametersCSVfile.png|500px|thumb|center|Example of Regression Computation Input CSV file]]
|}

===Shape4D Parameters===

====Time Parameters====

{|
|[[Image:RegressionComputation-TimeParameters.png|thumb|500px|Regression Computation Time Parameters]]
|This section allows the user to specify:
* The first and last time points of the input shapes
* The number of time-regressed shapes that will be computed between the first and last input shapes
|}

====Output Parameters====

{|
Shape4D CLI will compute several sets of time-regressed shapes where the basename of each shape will be: ''<prefix>_iter_n_time_00i'' with:
*<prefix>: the prefix can be specified by the user
* n: the iteration number of the shape regression process (i.e. represents the number of the time-regressed shape serie)
* i: the time-regressed shape number
The last iteration will create the final time-regressed shape set where the basename of the shapes will be ''<prefix>_final_time_00i''.
|[[Image:RegressionComputation-OutputParameters.png|thumb|500px|Regression Computation Output Parameters]]
|This section allows the user to specify :
* The output folder where the computed time-regressed shape sets will be stored
* The prefix of the basename of each time-regressed shapes
* The occurrence at which the time-regressed shapes set will be saved
|}

====Optimal Parameters====

{|
|[[Image:RegressionComputation-OptimalParameters.png|thumb|500px|Regression Computation Optimal Parameters]]
|This section allows the user to specify:
* The optimal method used by Shape4D CLI
* The minimum distance that will stopped the shape regression process
* The maximum number of iteration
|}

==Regression Visualization Module==

This module allows to easily visualize the results obtained by the RegressionComputation module by using severals slicer extensions ([[Documentation/{{documentation/version}}/Extensions/Sequences|Sequences]], [[Documentation/{{documentation/version}}/Modules/Colors|Colors]], [[Documentation/{{documentation/version}}/Modules/Tables|Tables]]).

===Inputs===

{|
This section allows the user to create a sequence containing the time-regressed shapes computed by RegressionComputation module.
|[[Image:RegressionVisualization-ShapeRegressionInputs.png|thumb|500px|Shape Regression Inputs]]
| In order to do that, the user would have to specify:
* The input directory which should contain the time-regressed shape sets computed by RegressionComputation module
* The rootname of the time-regressed shape set that should be ''<prefix>_iter_n_time_'' with:
** The prefix specified by the user in the RegressionComputation module
** n the iteration number of the shape regression process that the user want to visualize (''iter_n'' will be replaced by ''final'' if the user wants to display the final results computed)
|}

===Visualization===

====Sequence Visualization====

{|
|[[Image:RegressionVisualization-SequenceVisualizationOptions.png|thumb|500px|Sequence Visualization Options]]
| In this tab, the user could:
* customize the color maps of the shapes contained in the sequence
* navigate through the sequence thanks to a browser
[[Image:BrainGrowth_RegressionSequence.gif|450px|thumb|center|Example of a brain growth sequence]]
|}

====Regression Plot====

{|
This tab allows the user to plot the time-regressed shape volume evolution according to the time.
|[[Image:RegressionVisualization-RegressionPlot.png|thumb|500px|Regression Plot]]
| To do so, the user will have to specify the path of a CSV file containing the following information used to compute the set of time-regressed shapes in RegressionComputation module:
* The path of each input shape
* The time-point associated
|[[Image:BrainModelVolume_RegressionPlot.png|200px|thumb|center|Example of Regression Plot]]
|}


{{documentation/{{documentation/version}}/module-section|Additional Information}}

This extension is available on [https://www.slicer.org/ 3DSlicer] and on [http://salt.slicer.org/ SlicerSALT].


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
N/A


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
The source code is available on [https://github.com/KitwareMedical/ShapeRegressionExtension github]


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[[Category:Documentation/{{documentation/version}}/Modules/ShapeAnalysis]]

Documentation/4.10/Extensions/ShapeRegressionExtension - Revision history

UpdateBot: Nightly -> 4.10