Slicer Wiki - User contributions [en]

Documentation/Nightly/Extensions/ShapeRegressionExtension

2018-02-06T21:29:23Z

Lpascal:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{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}}

'''''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>

{{documentation/{{documentation/version}}/module-introduction-end}}

{{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]


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

Documentation/4.8/Extensions/ShapeRegressionExtension

2018-02-06T21:29:16Z

Lpascal:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{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}}

'''''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>

{{documentation/{{documentation/version}}/module-introduction-end}}

{{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 RegressionComputation 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]


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

Documentation/4.8/Extensions/ShapeRegressionExtension

2018-01-31T15:43:17Z

Lpascal:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{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}}

'''''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>

{{documentation/{{documentation/version}}/module-introduction-end}}

{{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 CSV files]]
|}

===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]


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

Documentation/Nightly/Extensions/ShapeRegressionExtension

2018-01-31T15:43:10Z

Lpascal:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{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}}

'''''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>

{{documentation/{{documentation/version}}/module-introduction-end}}

{{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 CSV files]]
|}

===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]


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

Documentation/Nightly/Extensions/ShapeRegressionExtension

2018-01-30T23:21:39Z

Lpascal:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{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}}

'''''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>

{{documentation/{{documentation/version}}/module-introduction-end}}

{{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 CSV files]]
|}

===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>_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>_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 (n will be ''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]


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

Documentation/4.8/Extensions/ShapeRegressionExtension

2018-01-30T23:21:17Z

Lpascal:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{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}}

'''''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>

{{documentation/{{documentation/version}}/module-introduction-end}}

{{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 CSV files]]
|}

===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>_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>_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 (n will be ''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]


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

Documentation/4.8/Extensions/ShapeRegressionExtension

2018-01-30T23:05:26Z

Lpascal: Created page with "<noinclude>{{documentation/versioncheck}}</noinclude>  {{documentation/{{documentation/version}}/module-header}} <!-- --------------------..."

<noinclude>{{documentation/versioncheck}}</noinclude>

{{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}}

'''''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>

{{documentation/{{documentation/version}}/module-introduction-end}}

{{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 [https://www.slicer.org/wiki/Documentation/Nightly/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 CSV files]]
|}

===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>_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 ([https://www.slicer.org/wiki/Documentation/Nightly/Extensions/Sequences Sequences], [https://www.slicer.org/wiki/Documentation/4.8/Modules/Colors Colors], [https://www.slicer.org/wiki/Documentation/Nightly/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>_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 (n will be ''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]


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

Documentation/Nightly/Extensions/ShapeRegressionExtension

2018-01-30T23:04:54Z

<noinclude>{{documentation/versioncheck}}</noinclude>

{{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}}

'''''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>

{{documentation/{{documentation/version}}/module-introduction-end}}

{{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 [https://www.slicer.org/wiki/Documentation/Nightly/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 CSV files]]
|}

===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>_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 ([https://www.slicer.org/wiki/Documentation/Nightly/Extensions/Sequences Sequences], [https://www.slicer.org/wiki/Documentation/4.8/Modules/Colors Colors], [https://www.slicer.org/wiki/Documentation/Nightly/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>_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 (n will be ''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]


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

File:RegressionComputation-InputShapeParameters.png

2018-01-29T23:26:14Z

Lpascal: Lpascal uploaded a new version of File:RegressionComputation-InputShapeParameters.png

File:RegressionComputation-InputShapeParameters.png

2018-01-29T23:11:53Z

Lpascal: Lpascal uploaded a new version of File:RegressionComputation-InputShapeParameters.png

File:RegressionComputation-OptimalParameters.png

2018-01-29T20:52:25Z

Lpascal:

File:RegressionComputation-OutputParameters.png

2018-01-29T20:52:07Z

Lpascal:

File:RegressionComputation-TimeParameters.png

2018-01-29T20:51:44Z

Lpascal:

File:RegressionVisualization-RegressionPlot.png

2018-01-29T20:24:54Z

Lpascal:

File:RegressionVisualization-SequenceVisualizationOptions.png

2018-01-29T20:24:25Z

Lpascal:

File:RegressionVisualization-ShapeRegressionInputs.png

2018-01-29T20:24:07Z

Lpascal:

File:BrainGrowth RegressionSequence.gif

2018-01-29T20:20:22Z

Lpascal:

File:BrainModelVolume RegressionPlot.png

2018-01-29T20:09:03Z

Lpascal:

File:RegressionComputation-ExampleInputShapeParametersCSVfile.png

2018-01-29T19:08:06Z

Lpascal:

File:RegressionComputation-InputShapeParameters.png

2018-01-29T19:00:01Z

Lpascal:

File:RegressionVisualization-Interface.png

2018-01-24T20:31:32Z

Lpascal:

File:RegressionComputation-Interface.png

2018-01-24T20:31:14Z

Lpascal:

Documentation/Nightly/Extensions/SpharmPdm

2017-12-21T17:30:23Z

Lpascal:

Documentation/4.8/Extensions/SpharmPdm

2017-12-21T17:28:39Z

Lpascal:

Documentation/Nightly/Extensions/SpharmPdm

2017-07-21T13:38:52Z

Lpascal:

Documentation/Nightly/Extensions/SpharmPdm

2017-06-22T20:45:41Z

Lpascal:

Documentation/Nightly/ModuleExtensionListing/Extensions by category

2017-06-22T16:02:14Z

Lpascal: /* Shape Analysis */

__NOTOC__
* [[#Extensions_by_category|Extensions by category]]
= Extensions by category =
33 categories:
* [[#Extensions_by_category_Astronomy|Astronomy]]
* [[#Extensions_by_category_Cardiac|Cardiac]]
* [[#Extensions_by_category_Cardiac_MRI_toolkit|Cardiac MRI toolkit]]
* [[#Extensions_by_category_Chest_Imaging_Platform|Chest Imaging Platform]]
* [[#Extensions_by_category_Converters|Converters]]
* [[#Extensions_by_category_Developer_Tools|Developer Tools]]
* [[#Extensions_by_category_DICOM|DICOM]]
* [[#Extensions_by_category_Diffusion|Diffusion]]
* [[#Extensions_by_category_Digital_Pathology|Digital Pathology]]
* [[#Extensions_by_category_Editor_Effects|Editor Effects]]
* [[#Extensions_by_category_Examples|Examples]]
* [[#Extensions_by_category_Exporter|Exporter]]
* [[#Extensions_by_category_Filtering|Filtering]]
* [[#Extensions_by_category_IGT|IGT]]
* [[#Extensions_by_category_Informatics|Informatics]]
* [[#Extensions_by_category_Libraries|Libraries]]
* [[#Extensions_by_category_Machine_Learning|Machine Learning]]
* [[#Extensions_by_category_Mesh_Generation|Mesh Generation]]
* [[#Extensions_by_category_Microscopy|Microscopy]]
* [[#Extensions_by_category_Nuclear_Medicine|Nuclear Medicine]]
* [[#Extensions_by_category_Quantification|Quantification]]
* [[#Extensions_by_category_Radiotherapy|Radiotherapy]]
* [[#Extensions_by_category_Registration|Registration]]
* [[#Extensions_by_category_Remote|Remote]]
* [[#Extensions_by_category_Scoliosis|Scoliosis]]
* [[#Extensions_by_category_Segmentation|Segmentation]]
* [[#Extensions_by_category_Sequences|Sequences]]
* [[#Extensions_by_category_Shape_Analysis|Shape Analysis]]
* [[#Extensions_by_category_Tractography|Tractography]]
* [[#Extensions_by_category_Training|Training]]
* [[#Extensions_by_category_Vascular_Modeling_Toolkit|Vascular Modeling Toolkit]]
* [[#Extensions_by_category_Web_System_Tools|Web System Tools]]
* [[#Extensions_by_category_Wizards|Wizards]]

== Astronomy ==
* [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]]

== Cardiac ==
* [[Documentation/Nightly/Extensions/SlicerHeart|SlicerHeart]]
* [http://brainsia.github.io/CardiacAgatstonMeasures/ CardiacAgatstonMeasures]

== Cardiac MRI toolkit ==
* [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit]

== Chest Imaging Platform ==
* [http://www.chestimagingplatform.org Chest_Imaging_Platform]

== Converters ==
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension]

== Developer Tools ==
* [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|DeveloperToolsForExtensions]]
* [[Documentation/Nightly/Extensions/DebuggingTools|DebuggingTools]]
* [[Documentation/Nightly/Extensions/MatlabBridge|MatlabBridge]]
* [[Documentation/Nightly/Extensions/ImageMaker|ImageMaker]]

== DICOM ==
* [[Documentation/Nightly/Extensions/DCMQI|DCMQI]]

== Diffusion ==
* [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]]
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]]

== Digital Pathology ==
* [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]]

== Editor Effects ==
* [[Documentation/Nightly/Extensions/WindowLevelEffect|WindowLevelEffect]]

== Examples ==
* [[Documentation/Nightly/Extensions/OpenCVExample|OpenCVExample]]

== Exporter ==
* [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|SlicerToKiwiExporter]]

== Filtering ==
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound]

== IGT ==
* [[Documentation/Nightly/Extensions/GyroGuide|GyroGuide]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/TrackerStabilizer TrackerStabilizer]
* [[Documentation/Nightly/Extensions/CornerAnnotation|CornerAnnotation]]
* [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]]
* [[Documentation/Nightly/Extensions/PercutaneousApproachAnalysis|PercutaneousApproachAnalysis]]
* [[Documentation/Nightly/Extensions/NeedleFinder|NeedleFinder]]
* [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]]
* [[Documentation/Nightly/Extensions/iGyne|iGyne]]
* [[Documentation/Nightly/Extensions/ResectionPlanner|ResectionPlanner]]

== Informatics ==
* [[Documentation/Nightly/Extensions/CurveMaker|CurveMaker]]
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|LongitudinalPETCT]]
* [[Documentation/Nightly/Extensions/mpReview|mpReview]]
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]]
* [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]]
* [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]]

== Libraries ==
* [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]]

== Machine Learning ==
* [[Documentation/Nightly/Extensions/DeepInfer|DeepInfer]]


== Mesh Generation ==
* [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC_3D_I2MConversion]]
* [[Documentation/Nightly/Extensions/CleaverExtension|CleaverExtension]]

== Microscopy ==
* [[Documentation/Nightly/Extensions/IASEM|IASEM]]

== Nuclear Medicine ==
* [http://gti-fing.github.io/SlicerPetSpectAnalysis PetSpectAnalysis]

== Quantification ==
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis]
* [[Documentation/Nightly/Extensions/ModelToModelDistance|ModelToModelDistance]]
* [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]]
* [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]]
* [[Documentation/Nightly/Extensions/DiceComputation|DiceComputation]]
* [[Documentation/Nightly/Extensions/PETLiverUptakeMeasurement|PETLiverUptakeMeasurement]]
* [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]]
* [[Documentation/Nightly/Extensions/PkModeling|PkModeling]]
* [[Documentation/Nightly/Extensions/ShapeVariationAnalyzer|ShapeVariationAnalyzer]]


== Radiotherapy ==
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/FilmDosimetry FilmDosimetryAnalysis]
* [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]]
* [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry GelDosimetryAnalysis]

== Registration ==
* [[Documentation/Nightly/Extensions/ScatteredTransform|ScatteredTransform]]
* [[Documentation/Nightly/Extensions/CMFreg|CMFreg]]
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]]
* [[Documentation/Nightly/Extensions/MultiLevelRegistration|MultiLevelRegistration]]


== Remote ==
* [[Documentation/Nightly/Extensions/XNATSlicer|XNATSlicer]]

== Scoliosis ==
* [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]]

== Segmentation ==
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutSegment]
* [http://www.nitrc.org/projects/abc ABC]
* [[Documentation/Nightly/Extensions/ROBEXBrainExtraction|ROBEXBrainExtraction]]
* [[Documentation/Nightly/Extensions/SwissSkullStripper|SwissSkullStripper]]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice]
* [[Documentation/Nightly/Extensions/SkullStripper|SkullStripper]]
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]]
* [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScarSegmenter]]
* [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects]
* [[Documentation/Nightly/Extensions/OpenCAD|OpenCAD]]
* [[Documentation/Nightly/Extensions/IntensitySegmenter|IntensitySegmenter]]
* [https://github.com/Tomnl/Slicer-Wasp Wasp]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation AirwaySegmentation]
* [[Documentation/Nightly/Extensions/SobolevSegmenter|SobolevSegmenter]]
* [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut FastGrowCutEffect]
* [[Documentation/Nightly/Extensions/VolumeClip|VolumeClip]]

== Sequences ==
* [[Documentation/Nightly/Extensions/Sequences|Sequences]]

== Shape Analysis ==
* [[Documentation/Nightly/Extensions/MeshToLabelMap|MeshToLabelMap]]
* [[Documentation/Nightly/Extensions/Q3DC|Q3DC]]
* [[Documentation/Nightly/Extensions/EasyClip|EasyClip]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint PickAndPaintExtension]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MeshStatistics MeshStatisticsExtension]
* [https://www.slicer.org/wiki/Documentation/Nightly/Extensions/SpharmPdm SPHARM-PDM]


== Tractography ==
* [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]]

== Training ==
* [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]]

== Vascular Modeling Toolkit ==
* [http://slicer.vmtk.org/ VMTK]

== Web System Tools ==
* [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractor]]

== Wizards ==
* [[Documentation/Nightly/Extensions/ChangeTracker|ChangeTracker]]
__NOTOC__

Documentation/Nightly/Extensions/ShapePopulationViewer

2016-02-02T17:38:57Z

Lpascal:

File:SPV1.png

2016-01-15T17:02:55Z

Lpascal: Lpascal uploaded a new version of File:SPV1.png

File:SPV attributeInfo.png

2016-01-15T16:37:12Z

Lpascal: Lpascal uploaded a new version of File:SPV attributeInfo.png

File:SPV fileInfo.png

2016-01-15T16:36:34Z

Lpascal: Lpascal uploaded a new version of File:SPV fileInfo.png

File:SPV vectors1.png

2016-01-15T16:30:59Z

Lpascal: Lpascal uploaded a new version of File:SPV vectors1.png

File:SPV colormap1.png

2016-01-15T16:27:50Z

Lpascal: Lpascal uploaded a new version of File:SPV colormap1.png

Documentation/Nightly/Extensions/ShapePopulationViewer

2016-01-14T21:25:35Z

Lpascal:

File:SPV10.png

2016-01-05T18:37:33Z

Lpascal: Color map by direction of a right condyle

Color map by direction of a right condyle

File:SPV9.png

2016-01-05T18:34:34Z

Lpascal: Window for customize the color map by direction

Window for customize the color map by direction