Difference between revisions of "Algorithm:MGH"

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== Coordination ==
+
Back to [[Algorithm:Main|NA-MIC Algorithms]]
  
[[Algorithm:MGH:Coordination:Meeting_2004-11-17|2004-11-17 meeting @ MGH]]
+
= Overview of MGH Algorithms =
  
[[Algorithm:MGH:Coordination:Meeting_2005-1-21|2005-1-21 meeting @ BWH]]
+
A brief overview of the MGH's algorithms goes here.  This should not be much longer than a paragraph.  Remember that people visiting your site want to be able to understand very quickly what you're all about and then they want to jump into your site's projects.  The projects below are organized into a two column table: the left column is for representative images and the right column is for project overviews.  The number of rows corresponds to the number of projects at your site.  Put the most interesting and relevant projects at the top of the table.  You do not need to organize the table according to subject matter (i.e. do not group all segmentation projects together and all DWI projects together).
  
== Projects ==
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= MGH Projects =
  
=== In Development ===
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{|
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| style="width:10%" | [[Image:placeholder.png|left|200px]]
 +
| style="width:90%" |
  
===='''QDEC: An easy to use GUI for group morphometry studies'''====
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== [[Algorithm:MGH:QDEC|QDEC: An easy to use GUI for group morphometry studies]] ==
* Difficulty: Medium
 
* Impact: High
 
* '''Use cases''': See [http://surfer.nmr.mgh.harvard.edu/fswiki/QdecProject Qdec project page]
 
  
* '''Use case'''<nowiki>: 'Compare the primary eigendirection in two groups to see if they are the same' </nowiki>
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Compare the primary eigendirection in two groups to see if they are the same.[[Algorithm:MGH:QDEC|More...]]
* Difficulty: Low
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* Impact: Medium
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<font color="red">'''New: '''</font> Put something new here.
  
 
See: [http://surfer.nmr.mgh.harvard.edu/fswiki/Qdec Qdec user page]
 
See: [http://surfer.nmr.mgh.harvard.edu/fswiki/Qdec Qdec user page]
  
====''''Optimal path calculator (Poistats)'''====
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|-
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| | [[Image:placeholder.png|thumb|left|200px]]
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| |
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== [[AHM_2006:ProjectsDTIPathOfInterest|Optimal path calculator (Poistats)]] ==
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 +
Provide software deliverable with robust support for input images with varying slice prescription, voxel size, tensor measurement frame, etc. Ensure compatibility with Slicer file formats and Dartmouth tensor data conventions. [[AHM_2006:ProjectsDTIPathOfInterest|More...]]
 +
 
 +
<font color="red">'''New: '''</font> Put something new here.
 +
 
 +
|-
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 +
| | [[Image:placeholder.png|thumb|left|200px]]
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| |
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== [[Engineering:Project:Non-rigid_EPI_registration|Engineering:Project:Non-rigid_EPI_registration]] ==
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 +
My objective is to evaluate the benefit of using ITK nonlinear registration for group FA comparisons. [[Engineering:Project:Non-rigid_EPI_registration|More...]]
 +
 
 +
<font color="red">'''New: '''</font> Put something new here.
  
* '''Use case'''<nowiki>: 'Specify 2 points in a diffusion image and tell how connected they are.' </nowiki>
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|-
* Difficulty: High
 
* Impact: High
 
  
See: [[AHM_2006:ProjectsDTIPathOfInterest|AHM 2006:ProjectsDTIPathOfInterest]]
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| | [[Image:placeholder.png|thumb|left|200px]]
 +
| |
  
===='''Statistical power benefit of ITK nonlinear registration'''====
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== [[Algorithm:MGH:NRDDFreesurfer|Adding NRRD I/O to Freesurfer]] ==
  
* '''Use case'''<nowiki>: 'Evaluate benefit of using ITK nonlinear registration for group FA comparisons' </nowiki>
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Our objective is to open a NRRD volume in FreeSurfer, and convert an MGH volume to a NRRD volume with Freesurfer. [[Algorithm:MGH:NRDDFreesurfer|More...]]
* Difficulty: Low-Medium
 
* Impact: Medium
 
  
See: [[Engineering:Project:Non-rigid_EPI_registration|Engineering:Project:Non-rigid_EPI_registration]]
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<font color="red">'''New: '''</font> Put something new here.
  
===='''Adding NRRD I/O to Freesurfer'''====
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|-
  
* '''Use case'''<nowiki>: 'Open a NRRD volume in FreeSurfer.' </nowiki>
+
| | [[Image:placeholder.png|thumb|left|200px]]
* '''Use case'''<nowiki>: 'Convert an MGH volume to a NRRD volume with Freesurfer.' </nowiki>
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| |
* Difficulty: Low
 
* Impact: Medium
 
  
# Write unit tests for new IO functions (Snyder): '''in progress'''
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== [[Algorithm:MGH:Development:SphericalWavelets|Spherical Wavelets]] ==
# Add NrrdIO libraries from Teem to FS source tree, build with autoconf (Snyder): '''done'''
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Cortical Surface Shape Analysis Based on Spherical Wavelets. [[Algorithm:MGH:Development:SphericalWavelets|More...]]
# Write and test FS NRRD IO functions (Snyder, Kindlmann): '''in progress'''
 
# Develop approriate headers for MGH DWI data (Teich): '''queued'''
 
# Automate header generation when possible (Teich): '''queued'''
 
  
===='''Cortical Surface Shape Analysis Based on Spherical Wavelets'''====
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<font color="red">'''New: '''</font> IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007
  
See: [[Algorithm:MGH:Development:SphericalWavelets|Algorithm:MGH:SphericalWavelets]]
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|-
  
===='''Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops'''====
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| | [[Image:placeholder.png|thumb|left|200px]]
 +
| |
  
See: [[Algorithm:MGH:Development:TopologyCorrection|Algorithm:MGH:Development:TopologyCorrection]]
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== [[Algorithm:MGH:Development:TopologyCorrection|Topology Correction]] ==
 +
Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops. [[Algorithm:MGH:Development:TopologyCorrection|More...]]
 +
 
 +
<font color="red">'''New: '''</font> IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007
  
 
<br />
 
<br />
  
* '''queued''' - step identified/specd
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|-
* '''in progress''' - step in progress
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* '''done''' - step complete
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| | [[Image:placeholder.png|thumb|left|200px]]
 +
| |
 +
 
 +
== [[Algorithm:MGH:QBALLVisualization|QBall Visualization]] ==
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 +
Our objective is to visualize q-ball data in Slicer. [[Algorithm:MGH:QBALLVisualization|More...]]
  
=== Done ===
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<font color="red">'''New: '''</font> Put something new here.
  
===='''QBALL visualization'''====
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|-
  
* '''Use case'''<nowiki>: 'Visualize q-ball data in Slicer.' </nowiki>
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| | [[Image:placeholder.png|thumb|left|200px]]
* Difficulty: Low
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| |
* Impact: Medium
 
  
# Implement ODF polygon decimation algorithm (Tuch) : '''done'''
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== [[Algorithm:MGH:Development:GroupComp|Tensor-based group comparison (Cramer test)]] ==
# Port decimation fileformat into FreeDiffusion Visualizer (Snyder) : '''done'''
 
# Port QBALL/ODF visualization into [[Slicer|Slicer]] (Estepar/Snyder/Kindlmann/Tuch/Westin): '''done'''
 
## Implement (Estepar): '''done'''
 
## Test on mock data set (Estepar): '''done'''
 
## Demo for real data set (Estepar/Snyder/Kindlmann): '''done'''
 
  
===='''Tensor-based group comparison (Cramer test)'''====
+
Our objective is to boost statistical sensitivity for group comparisons in comparison to 'traditional' univariate tests. [[Algorithm:MGH:Development:GroupComp|More...]]
  
* '''Use case'''<nowiki>: 'Compare DTI images between groups using the full tensor information.' </nowiki>
+
<font color="red">'''New: '''</font> Paper submitted: "Statistical Group Comparison of Diffusion Tensors via Multivariate Hypothesis Testing."
* Difficulty: Medium
 
* Impact: Medium-High
 
  
# Implement in R (Whitcher/Tuch) : '''done'''
+
|-
# Power analysis (Whitcher) : '''done'''
 
# Port to Matlab (Whitcher) : '''done'''
 
# Validate Matlab version against R (Whitcher) : '''done'''
 
# Test on group data : '''done'''
 
# Release bootstrap-only version to test group: '''done'''
 
# Port FFT method from R to matlab (Whitcher): '''done'''
 
# Implement FFT method in diffusion development environment (Tuch): '''done'''
 
  
See [[Algorithm:MGH:Development:GroupComp|Algorithm:MGH:Development:GroupComp]]
+
| | [[Image:placeholder.png|thumb|left|200px]]
 +
| |
  
===='''Replacing Numerical Recipes in FreeSurfer (for open sourcing)'''====
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== [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|Numerical Recipies Replacement]] ==
  
* '''Use case'''<nowiki>: 'Unit tests pass with all replacements.' </nowiki>
+
Our obejective is to replace algorithms using proprietary numerical recipes in FreeSurfer in efforts to open source FreeSurfer. [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|More...]]
* Difficulty: Medium-High
 
* Impact: High
 
  
# Write test cases for each algorithm (Snyder, Jen): '''done'''
+
<font color="red">'''New: '''</font> Completed
# Identify replacements (Snyder, Jen): '''done'''
 
# Integrate required libraries into FreeSurfer build process (Snyder, Jen): '''done'''
 
# Iteratively replace recipes with substitutes and run tests (Snyder, Jen): '''done'''
 
  
See: [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|Numerical Recipies Replacement]]
+
|-
  
===='''Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms'''====
+
| | [[Image:placeholder.png|thumb|left|200px]]
 +
| |
  
* '''Use Case'''<nowiki>: 'Atlas-based fully automated whole brain segmentation' </nowiki>
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== [[Algorithm:MGH:Development:AutoBrainSeg|Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms]] ==
* Difficulty: Medium-High
 
* Impact: Medium-High
 
  
# Implemented in C and distribute with the FreeSurface Package: '''done'''
+
Atlas-based approaches have demonstrated the ability to automatically identify detailed brain structures from 3-D magnetic resonance (MR) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse sequence than the data used for the atlas training. In this paper, we improve the performance of an atlas-based whole brain segmentation method by introducing an intensity renormalization procedure that automatically adjusts the prior atlas intensity model to new input data. Validation using manually labeled test datasets has shown that the new procedure improves the segmentation accuracy (as measured by the Dice coefficient) by 10% or more for several structures including hippocampus, amygdala, caudate, and pallidum. The results verify that this new procedure reduces the sensitivity of the whole brain segmentation method to changes in scanner platforms and improves its accuracy and robustness, which can thus facilitate multicenter or multisite neuroanatomical imaging studies. [[Algorithm:MGH:Development:AutoBrainSeg|More...]]
  
See: [[Algorithm:MGH:Development:AutoBrainSeg|Algorithm:MGH:Development:AutoBrainSeg]]
+
<font color="red">'''New: '''</font> IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007

Revision as of 19:37, 27 November 2007

Home < Algorithm:MGH
Back to NA-MIC Algorithms

Overview of MGH Algorithms

A brief overview of the MGH's algorithms goes here. This should not be much longer than a paragraph. Remember that people visiting your site want to be able to understand very quickly what you're all about and then they want to jump into your site's projects. The projects below are organized into a two column table: the left column is for representative images and the right column is for project overviews. The number of rows corresponds to the number of projects at your site. Put the most interesting and relevant projects at the top of the table. You do not need to organize the table according to subject matter (i.e. do not group all segmentation projects together and all DWI projects together).

MGH Projects

File:Placeholder.png

QDEC: An easy to use GUI for group morphometry studies

Compare the primary eigendirection in two groups to see if they are the same.More...

New: Put something new here.

See: Qdec user page

File:Placeholder.png

Optimal path calculator (Poistats)

Provide software deliverable with robust support for input images with varying slice prescription, voxel size, tensor measurement frame, etc. Ensure compatibility with Slicer file formats and Dartmouth tensor data conventions. More...

New: Put something new here.

File:Placeholder.png

Engineering:Project:Non-rigid_EPI_registration

My objective is to evaluate the benefit of using ITK nonlinear registration for group FA comparisons. More...

New: Put something new here.

File:Placeholder.png

Adding NRRD I/O to Freesurfer

Our objective is to open a NRRD volume in FreeSurfer, and convert an MGH volume to a NRRD volume with Freesurfer. More...

New: Put something new here.

File:Placeholder.png

Spherical Wavelets

Cortical Surface Shape Analysis Based on Spherical Wavelets. More...

New: IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007

File:Placeholder.png

Topology Correction

Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops. More...

New: IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007


File:Placeholder.png

QBall Visualization

Our objective is to visualize q-ball data in Slicer. More...

New: Put something new here.

File:Placeholder.png

Tensor-based group comparison (Cramer test)

Our objective is to boost statistical sensitivity for group comparisons in comparison to 'traditional' univariate tests. More...

New: Paper submitted: "Statistical Group Comparison of Diffusion Tensors via Multivariate Hypothesis Testing."

File:Placeholder.png

Numerical Recipies Replacement

Our obejective is to replace algorithms using proprietary numerical recipes in FreeSurfer in efforts to open source FreeSurfer. More...

New: Completed

File:Placeholder.png

Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms

Atlas-based approaches have demonstrated the ability to automatically identify detailed brain structures from 3-D magnetic resonance (MR) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse sequence than the data used for the atlas training. In this paper, we improve the performance of an atlas-based whole brain segmentation method by introducing an intensity renormalization procedure that automatically adjusts the prior atlas intensity model to new input data. Validation using manually labeled test datasets has shown that the new procedure improves the segmentation accuracy (as measured by the Dice coefficient) by 10% or more for several structures including hippocampus, amygdala, caudate, and pallidum. The results verify that this new procedure reduces the sensitivity of the whole brain segmentation method to changes in scanner platforms and improves its accuracy and robustness, which can thus facilitate multicenter or multisite neuroanatomical imaging studies. More...

New: IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007