DBP2:UNC:Cortical Thickness Roadmap - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T17:00:58Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Cvachet: /* Schedule */

2010-08-27T20:35:56Z

Schedule

Cvachet: /* Overview */

2010-08-27T20:21:04Z

Overview

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Overview

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2010-08-27T18:17:04Z

Overview

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Schedule

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Schedule

Cvachet: /* Local correspondence */

2010-08-27T16:32:40Z

Local correspondence

Cvachet: /* Overview */

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Overview

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Overview

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 === White matter/gray matter segmentation ===
-:* UNC has an open source segmentation tool called itkEMS ([http://www.ia.unc.edu/dev/download/itkems/index.htm binary download]) implemented in an ITK framework for segmenting white matter and gray matter in the young brain. An initial Slicer3 [http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation command line module] was implemented and works well. This initial Slicer3 command line module is based on the existing itkEMS xml I/O for parameters. A more extensive adaptation that would allow the direct modification of the itkEMS parameters within Slicer3 is in discussion.
+:* UNC has an open source segmentation tool called itkEMS ([http://www.ia.unc.edu/dev/download/itkems/index.htm binary download]) implemented in an ITK framework for segmenting white matter and gray matter in the young brain. An initial Slicer3 [https://www.slicer.org/wiki/Slicer3:Execution_Model_Documentation command line module] was implemented and works well. This initial Slicer3 command line module is based on the existing itkEMS xml I/O for parameters. A more extensive adaptation that would allow the direct modification of the itkEMS parameters within Slicer3 is in discussion.
 :** Since this segmentation technique exists in an ITK framework, the integration into Slicer3 was low risk and has been completed.
-:* UNC also adapts the current [[http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation Slicer3 EM Segment module]] to their young brain studies.  Here, UNC adapted their UNC atlas of the 2 year old brain to provide priors for the EM Segment module. Initial tests have been successful, but more tests are needed.
+:* UNC also adapts the current [[https://www.slicer.org/wiki/Slicer3:Execution_Model_Documentation Slicer3 EM Segment module]] to their young brain studies.  Here, UNC adapted their UNC atlas of the 2 year old brain to provide priors for the EM Segment module. Initial tests have been successful, but more tests are needed.
 :** This is a good test case for applying the Slicer3 EM Segment module to a slightly different application. UNC worked through the training material on the Slicer3 EM Segment module and discussed open issues regularly with Brad Davis (as well as Kilian Pohl).
 :* A [[DBP2:UNC:Tissue_Segmentation_Evaluation | tissue segmentation evaluation]] was performed to compare both algorithms: itkEMS and EMSegment
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 :* '''10/15/2007''' - White matter/gray matter segmentation of the young brain using itkEMS as a Slicer3 module (C Vachet)  -- DONE --
 :* '''01/01/2008''' - White matter/gray matter segmentation of the young brain using the Slicer3 EM Segment module (C Vachet)  -- DONE --
-:* '''01/02/2008''' - Separate use case scenario wiki page: how to adjust/adapt the atlas definition in the EM Segment module ([http://www.slicer.org/slicerWiki/index.php/Modules:EM-Segmenter-Documentation:FAQ EMSegment FAQ]) (S Jaume) -- DONE --
+:* '''01/02/2008''' - Separate use case scenario wiki page: how to adjust/adapt the atlas definition in the EM Segment module ([https://www.slicer.org/wiki/Modules:EM-Segmenter-Documentation:FAQ EMSegment FAQ]) (S Jaume) -- DONE --
 :* '''01/07/2008''' - Registration to atlas in EM Segment (B Davis) -- DONE --
 :* '''02/15/2008''' - [[DBP2:UNC:Tissue_Segmentation_Evaluation | Comparison study itkEMS vs EM Segment in Slicer 3]] (C Vachet) -- DONE --

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 :* '''10/01/2008''' - Inflation/Unfolding module tested on cortical data (C Vachet)  -- DONE --
 :* '''06/01/2008''' - Slicer 3 module for cortical correspondence on inflated surface (I Oguz) -- DONE --
-:* '''04/01/2009''' - Evaluation of regional cortical thickness computation on small set of autism DBP datasets (C Vachet, C Mathieu) -- DONE --
+:* '''04/01/2009''' - [[DBP2:UNC:Cortical_Thickness_Comparison | Evaluation of regional cortical thickness computation on small set of autism DBP datasets]] (C Vachet, C Mathieu) -- DONE --
 * Statistical analysis and Hypothesis testing
 :* '''09/01/2008''' - GLM model for UNC statistical shape analysis (M Styner, N Augier, M Niethammer, M Macenco) -- DONE --
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 * Workflow/cohesive tools
 :* '''06/01/2008''' - Slicer 3 Workflow Shape Analysis module (C Vachet, N Augier) -- DONE ---
-:* '''10/01/2008''' - Individual regional analysis of cortical thickness as a single high-level Slicer3 module (C Vachet, C Mathieu) -- DONE --
+:* '''10/01/2008''' - [[DBP2:UNC:Regional_Cortical_Thickness_Pipeline | Individual regional analysis of cortical thickness as a single high-level Slicer3 module]] (C Vachet, C Mathieu) -- DONE --
-:* '''09/01/2009''' - Individual local analysis of cortical thickness as a single high-level Slicer3 module (C Vachet) -- DONE --
+:* '''01/01/2010''' - [[DBP2:UNC:Local_Cortical_Thickness_Pipeline | Group-wise mesh-based analysis of cortical thickness as a NA-MIC Workflow]] (C Vachet) -- DONE --
 == Team and Institute ==

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 :***This module has been tested on a small dataset.
 :***Pearson correlation analysis has been performed on an adult dataset to compare ARCTIC with state of the art (FreeSurfer)
 :* [[DBP2:UNC:Local_Cortical_Thickness_Pipeline | Local cortical thickness pipeline]]
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 <center>
 {|
-|[[Image:T1Image.jpg|thumb|250px|T1-weighted skull-stripped image]]
+|[[Image:GAMBIT QC CorticalThickness.png|thumb|500px|Cortical thickness overlayed on inflated cortical surfaces]]
-|valign="center"|[[Image:Parcellation.jpg|thumb|250px|Parcellation image]]
+|valign="center"|[[Image:GAMBIT_QC_SulcalDepth.png|thumb|500px|Sucal depth overlayed on inflated cortical surfaces]]
 |}
 </center>
 Next we discuss the main modules and details of current status and development work:

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 :***ARCTIC is available to the community via NITRC.
 :***This module has been tested on a small dataset.
-:***[[DBP2:UNC:Cortical_Thickness_Comparison | Pearson correlation analysis]] has been performed on an adult dataset to compare ARCTIC with state of the art (FreeSurfer)
+:***Pearson correlation analysis has been performed on an adult dataset to compare ARCTIC with state of the art (FreeSurfer)
 :* [[DBP2:UNC:Local_Cortical_Thickness_Pipeline | Local cortical thickness pipeline]]

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 :***ARCTIC is available to the community via NITRC.
 :***This module has been tested on a small dataset.
-:***Pearson correlation analysis has been performed on an adult dataset to compare ARCTIC with state of the art (FreeSurfer)
+:***[[DBP2:UNC:Cortical_Thickness_Comparison | Pearson correlation analysis]] has been performed on an adult dataset to compare ARCTIC with state of the art (FreeSurfer)
 :* [[DBP2:UNC:Local_Cortical_Thickness_Pipeline | Local cortical thickness pipeline]]

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 :* '''12/23/2007''' - UNC Cortical thickness measurement as a Slicer3 module (C Vachet) -- DONE --
 :* '''09/01/2008''' - Niethammer's Laplacian Cortical thickness measurement module code working at UNC as a Slicer3 module (C Vachet) -- DONE --
-:* '''09/15/2008''' - Regional comparison between UNC and Laplacian cortical thickness (C Vachet) -- IN PROGRESS --
+:* '''09/15/2008''' - Regional comparison between UNC and Laplacian cortical thickness (C Vachet) -- DONE --
 * Cortical correspondence
 :* '''08/15/2008''' - Slicer 3 Deformable registration of young brain regional atlas (C Vachet, C Mathieu) -- DONE --

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 :* Regional as well as local subject comparisons are needed.
 :* Regional analysis will require precise deformable registration to a young brain atlas.
-:** NA-MIC toolkit can be applied here, Slicer 3 has a b-spline based MI registration which needs to be tested.
+:** NA-MIC toolkit can be applied here, Slicer 3 has a B-spline based MI registration which needs to be tested.
 :*** The Slicer 3 registration modules have no possibility to save/load the computed transform (only the transformed image is saved), this is a necessity for this application!
 :*** This is an issue for both rigid, affine and b-spline based registration (all of these are needed for the full pipeline).
 :*** Testing will be performed to see whether registration quality is appropriate
 :*** An initial framework for the storage/retrieval and application of linear transforms has been implemented, and tests at UNC will soon take place.
-:** Parcellation atlas for regional analysis is the current atlas used by the DBP.
+:*** Report: Slicer3 modules (RegisterImages and ResampleScalar/Vector/DWIVolume) which allow atlas registration and image resampling are employed.
 :* Local analysis requires techniques which are not currently in the NA-MIC Kit, specifically a point-to-point correspondence on the cortex (either white/gray or gray/csf) boundary needs to be established.
 :** Freesurfer can be used for the local analysis (but it is not in the NA-MIC Kit).
 :** Ipek Oguz is developing local analysis tools and should be available in Fall 2008. The tool necessitates the following steps (also performed within Freesurfer):
 :*# Spherical topology of white matter: Marc Niethammer has developped a Slicer module for this step, testing will be necessary to ensure appropriateness in the cortical case. Initial tests of that module were successful.
-:*# Inflation of cortical surface: A Slicer module exists for this step, but likely not with the right properties. Tests and possible additional implementation will need to be done.
+:*# Inflation of cortical surface: a Slicer module exists for this step, but likely not with the right properties. DBP has implemented a Slicer3 module, with successful tests on our dataset.
 :*# Computation of correspondence on inflated surface using particle system: No module exists, a first command line prototype tool has been developed in collaboration with Utah (I Oguz, J Cates). Initial tests have shown to be very promising (ISBI 08 submission).

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 Ultimately, the NA-MIC Kit will provide a workflow for individual and group analysis of cortical thickness. It will be implemented as a set of Slicer3 modules that can be used interactively within the Slicer3 application as well as in batch on a computing cluster using BatchMake.
-Two pipelines are currently in development:
+Two pipelines have been developped:
 :* [[DBP2:UNC:Regional_Cortical_Thickness_Pipeline | Regional cortical thickness pipeline]]
 :**Current status:
-:***A Slicer3 high-level module (ARCTIC) has been developped to perform an individual lobar cortical thickness analysis.
+:***A Slicer3 high-level module (ARCTIC) has been developed that allows individual lobar cortical thickness analysis.
 :***This module has been tested on a small dataset.
 :***Pearson correlation analysis has been performed on an adult dataset to compare ARCTIC with state of the art (FreeSurfer)
 :* [[DBP2:UNC:Local_Cortical_Thickness_Pipeline | Local cortical thickness pipeline]]
-:**Current status: The pipeline is almost done. The last steps are still in testing mode.
+:**Current status:
-:***A Slicer3 high-level module (GAMBIT) has been developped to perform group-wise automatic mesh-based analysis of cortical thickness.
+:***A Slicer3 high-level module (GAMBIT) has been developed that allows group-wise automatic mesh-based analysis of cortical thickness.
 :***This module has been tested on a small dataset.