Melonakos at 20:51, 5 November 2008

2008-11-05T20:51:40Z

Andy: Update from Wiki

2006-12-18T13:17:25Z

Update from Wiki

New page

* '''Optimal path calculator'''
* '''Use case'''<nowiki>: 'Specify 2 points in a diffusion image and tell how connected they are.' </nowiki>
* Difficulty: High
* Impact: High

See [[AHM_2006:ProjectsDTIPathOfInterest|AHM 2006:ProjectsDTIPathOfInterest]]

 

* '''Statistical power benefit of ITK nonlinear registration'''
* '''Use case'''<nowiki>: 'Evaluate benefit of using ITK nonlinear registration for group FA comparisons' </nowiki>
* Difficulty: Low-Medium
* Impact: Medium

See: [[Engineering:Project:Non-rigid_EPI_registration|Engineering:Project:Non-rigid_EPI_registration]]

 

* '''Automatic segmentation of DTI using Spectral Clustering'''
* '''Use case'''<nowiki>: 'Automatically segment DTI image.' </nowiki>
* Difficulty: Medium-High
* Impact: Medium-High

# Implement algorithm in Matlab (Ziyan) : '''done'''
# Test/optimize on group data (Ziyan): '''in progress'''
# Port to diffusion toolkit (Tuch) : '''queued'''

 

* '''Replacing Numerical Recipes in FreeSurfer (for open sourcing)'''
* '''Use case'''<nowiki>: 'Unit tests pass with all replacements.' </nowiki>
* Difficulty: Medium-High
* Impact: High

# Write test cases for each algorithm (Snyder, Jen): '''done'''
# 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): '''in progress'''

 

* '''Adding NRRD I/O to Freesurfer'''
* '''Use case'''<nowiki>: 'Open a NRRD volume in FreeSurfer.' </nowiki>
* '''Use case'''<nowiki>: 'Convert an MGH volume to a NRRD volume with Freesurfer.' </nowiki>
* Difficulty: Low
* Impact: Medium

# Write unit tests for new IO functions (Snyder): '''in progress'''
# Add NrrdIO libraries from Teem to FS source tree, build with autoconf (Snyder): '''done'''
# Write and test FS NRRD IO functions (Snyder, Kindlmann): '''in progress'''
# Develop approriate headers for MGH DWI data (Snyder): '''queued'''
# Automate header generation when possible (Snyder): '''queued'''

 

* '''Replacing FreeDiffusion components with NA-MIC equivalents'''
* Difficulty: Medium-High
* Impact: Low

# Write regression tests: '''done'''
# Identify componenets to replace: '''queued'''
# Replace and test: '''queued'''

 

* '''queued''' - step identified/specd
* '''in progress''' - step in progress
* '''done''' - step complete

 

----

'''DONE'''

* '''QBALL visualization'''
* '''Use case'''<nowiki>: 'Visualize q-ball data in Slicer.' </nowiki>
* Difficulty: Low
* Impact: Medium

# Implement ODF polygon decimation algorithm (Tuch) : '''done'''
# 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'''

'''DONE'''

* '''Tensor-based group comparison (Cramer test)'''
* '''Use case'''<nowiki>: 'Compare DTI images between groups using the full tensor information.' </nowiki>
* 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]]

@@ Line 81: / Line 81: @@
 # Implement ODF polygon decimation algorithm (Tuch) : '''done'''
 # Port decimation fileformat into FreeDiffusion Visualizer (Snyder) : '''done'''
-# Port QBALL/ODF visualization into [[Slicer|Slicer]] (Estepar/Snyder/Kindlmann/Tuch/Westin): '''done'''
+# Port QBALL/ODF visualization into [[SlicerSummary|Slicer]] (Estepar/Snyder/Kindlmann/Tuch/Westin): '''done'''
 ## Implement (Estepar): '''done'''
 ## Test on mock data set (Estepar): '''done'''

Algorithm:MGH:Development - Revision history

Melonakos at 20:51, 5 November 2008

Andy: Update from Wiki