2008 Summer Project Week:RegionalCorticalThicknessTool - Revision history

Cvachet at 18:56, 30 June 2008

2008-06-30T18:56:42Z

Cvachet: /* Key Investigators */

2008-06-27T13:47:17Z

Key Investigators

Cvachet: /* Key Investigators */

2008-06-27T13:45:59Z

Key Investigators

Cvachet: /* Key Investigators */

2008-06-27T13:36:42Z

Key Investigators

Cvachet: /* Key Investigators */

2008-06-23T17:08:56Z

Key Investigators

Cvachet: /* Key Investigators */

2008-06-23T17:03:33Z

Key Investigators

Cvachet: New page: {| |Project Week Main Page ]] |} NOTOC ===Key Investigators=== * UNC: Heather Cody Hazlett, Martin St...

2008-06-11T19:48:18Z

New page: {| |thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page ]] |} __NOTOC__ ===Key Investigators=== * UNC: Heather Cody Hazlett, Martin St...

New page

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|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
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__NOTOC__

===Key Investigators===
* UNC: Heather Cody Hazlett, Martin Styner, Clement Vachet
* GE: Jim Miller

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<h1>Objective</h1>

We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of regional and local cortical thickness.

Such a workflow applied to the young brain (2-4 years old) is our goal in order to start a longitudinal study of early brain development in [[DBP2:UNC|autism (UNC DBP)]].

See our [[DBP2:UNC:Cortical_Thickness_Roadmap| Roadmap]] for more details.

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<h1>Approach, Plan</h1>

Our plan for the project week is to continue the development of a work flow tool allowing regional cortical thickness. This software executes a BatchMake script and runs several tools as threads.
Could the GUI be in FLTK, or should it be using KWWidget?
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<h1>Progress</h1>

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@@ Line 35: / Line 35: @@
 * Lobar parcellation registration
 ** Atlas to case affine registration: AffineRegistration module
-** Atlas to case BSPline registration: Deformable BSpline registration module
+** Atlas to case BSpline registration: Deformable BSpline registration module
 ** Applying transformation to parcellation map: Resample Volume 2 module
 * Cortical Thickness: CortthickCLP (UNC Slicer3 external module)

@@ Line 44: / Line 44: @@
 <h1>Progress</h1>
 Attended:
-* Special topic breakout: Non-rigid registration
+* Special topic breakout: Non-rigid registration (interested in RegisterImages module)
 * Special topic breakout: GWE
-The regional cortical thickness workflow has been developped using the module chaining method.
+The regional cortical thickness workflow has been developped using the module chaining method (Help from Marco Ruiz).
-Help from Marco Ruiz
+One part of the pipeline needs to be continued (skull stripping step)
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@@ Line 31: / Line 31: @@
 Our plan for the project week is to start the development of a work flow tool allowing regional cortical thickness analysis.
 Pipeline:
- - Tissue segmentation: itkEMSCLP UNC external Slicer3 module
+* Tissue segmentation: itkEMSCLP (UNC external Slicer3 module)
- - Skull Stripping: in progress (UNC Slicer3 external modules) - ImageMath and SegPostProcess Slicer3 modules
+* Skull Stripping: ImageMath and SegPostProcess (UNC Slicer3 external modules) - in progress
- - Lobar parcellation registration
+* Lobar parcellation registration
-   - Atlas to case affine registration: AffineRegistration module
+** Atlas to case affine registration: AffineRegistration module
-   - Atlas to case BSPline registration: Deformable BSpline registration module
+** Atlas to case BSPline registration: Deformable BSpline registration module
-   - Applying transformation to parcellation map: Resample Volume 2 module
+** Applying transformation to parcellation map: Resample Volume 2 module
- - Cortical Thickness: CortthickCLP (UNC Slicer3 external module)
+* Cortical Thickness: CortthickCLP (UNC Slicer3 external module)
 </div>
@@ Line 44: / Line 44: @@
 <h1>Progress</h1>
 Attended:
- - Special topic breakout: Non-rigid registration
+* Special topic breakout: Non-rigid registration
- - Special topic breakout: GWE
+* Special topic breakout: GWE
 </div>

@@ Line 29: / Line 29: @@
 <h1>Approach, Plan</h1>
-Our plan for the project week is to start the development of a work flow tool allowing regional cortical thickness analysis. This software executes a BatchMake script and runs several tools as threads.
+Our plan for the project week is to start the development of a work flow tool allowing regional cortical thickness analysis.
-Should it be a KWWidget application, or should we use a wizard workflow? Meeting with Ron and Jim...
+Pipeline:
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@@ Line 36: / Line 43: @@
 <h1>Progress</h1>
+Attended:

@@ Line 30: / Line 30: @@
 Our plan for the project week is to start the development of a work flow tool allowing regional cortical thickness analysis. This software executes a BatchMake script and runs several tools as threads.
-Should it be a KWWidget application, or should we use a wizard? Meeting with Ron and Jim...
+Should it be a KWWidget application, or should we use a wizard workflow? Meeting with Ron and Jim...
 </div>

2008 Summer Project Week:RegionalCorticalThicknessTool - Revision history

Cvachet at 18:56, 30 June 2008

Cvachet: /* Key Investigators */

Cvachet: /* Key Investigators */

Cvachet: /* Key Investigators */

Cvachet: /* Key Investigators */

Cvachet: /* Key Investigators */

Cvachet: New page: {| |Project Week Main Page ]] |} __NOTOC__ ===Key Investigators=== * UNC: Heather Cody Hazlett, Martin St...

Cvachet: New page: {| |Project Week Main Page ]] |} NOTOC ===Key Investigators=== * UNC: Heather Cody Hazlett, Martin St...