Algorithm:MGH:New - Revision history

JChris.FillionR: Fix MediaWiki table formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)

2023-04-11T06:07:48Z

Fix MediaWiki table formatting issue discovered while converting to GitHub Flavored Markdown using pandoc (via https://github.com/outofcontrol/mediawiki-to-gfm)

Melonakos at 19:36, 27 November 2007

2007-11-27T19:36:15Z

Melonakos at 20:21, 20 September 2007

2007-09-20T20:21:18Z

Melonakos at 18:48, 20 September 2007

2007-09-20T18:48:05Z

Melonakos at 18:43, 20 September 2007

2007-09-20T18:43:37Z

Melonakos at 18:40, 20 September 2007

2007-09-20T18:40:43Z

Melonakos at 18:34, 20 September 2007

2007-09-20T18:34:46Z

Melonakos at 02:24, 20 September 2007

2007-09-20T02:24:43Z

Melonakos at 02:05, 20 September 2007

2007-09-20T02:05:01Z

Melonakos at 01:53, 20 September 2007

2007-09-20T01:53:03Z

← Older revision		Revision as of 06:07, 11 April 2023
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	<font color="red">'''New: '''</font> IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007		<font color="red">'''New: '''</font> IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007
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← Older revision		Revision as of 19:36, 27 November 2007
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−	Back to [[Algorithm:Main\|NA-MIC Algorithms]]	+	Back to [[Algorithm:Main\|NA-MIC Algorithms]]

	= Overview of MGH Algorithms =		= Overview of MGH Algorithms =

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 Our objective is to boost statistical sensitivity for group comparisons in comparison to 'traditional' univariate tests. [[Algorithm:MGH:Development:GroupComp|More...]]
-<font color="red">'''New: '''</font> Put something new here.
+<font color="red">'''New: '''</font> Paper submitted: "Statistical Group Comparison of Diffusion Tensors via Multivariate Hypothesis Testing."
 |-
@@ Line 105: / Line 105: @@
 Our obejective is to replace algorithms using proprietary numerical recipes in FreeSurfer in efforts to open source FreeSurfer. [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|More...]]
-<font color="red">'''New: '''</font> Put something new here.
+<font color="red">'''New: '''</font> Completed
 |-
@@ Line 116: / Line 116: @@
 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...]]
-<font color="red">'''New: '''</font> Put something new here.
+<font color="red">'''New: '''</font> IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007

@@ Line 60: / Line 60: @@
 Cortical Surface Shape Analysis Based on Spherical Wavelets. [[Algorithm:MGH:Development:SphericalWavelets|More...]]
-<font color="red">'''New: '''</font> Put something new here.
+<font color="red">'''New: '''</font> IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007
 |-
@@ Line 70: / Line 70: @@
 Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops. [[Algorithm:MGH:Development:TopologyCorrection|More...]]
-<font color="red">'''New: '''</font> Put something new here.
+<font color="red">'''New: '''</font> IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007
 <br />

@@ Line 14: / Line 14: @@
 Compare the primary eigendirection in two groups to see if they are the same.[[Algorithm:MGH:QDEC|More...]]
 See: [http://surfer.nmr.mgh.harvard.edu/fswiki/Qdec Qdec user page]
@@ Line 25: / Line 27: @@
 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...]]
 |-
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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...]]
 |-
@@ Line 43: / Line 49: @@
 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...]]
 |-
@@ Line 50: / Line 59: @@
 == [[Algorithm:MGH:Development:SphericalWavelets|Spherical Wavelets]] ==
 Cortical Surface Shape Analysis Based on Spherical Wavelets. [[Algorithm:MGH:Development:SphericalWavelets|More...]]
 |-
@@ Line 58: / Line 69: @@
 == [[Algorithm:MGH:Development:TopologyCorrection|Topology Correction]] ==
 Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops. [[Algorithm:MGH:Development:TopologyCorrection|More...]]
 <br />
@@ Line 69: / Line 82: @@
 Our objective is to visualize q-ball data in Slicer. [[Algorithm:MGH:QBALLVisualization|More...]]
 |-
@@ Line 78: / Line 93: @@
 Our objective is to boost statistical sensitivity for group comparisons in comparison to 'traditional' univariate tests. [[Algorithm:MGH:Development:GroupComp|More...]]
 |-
@@ Line 87: / Line 104: @@
 Our obejective is to replace algorithms using proprietary numerical recipes in FreeSurfer in efforts to open source FreeSurfer. [[Algorithm:MGH:FreeSurferNumericalRecipiesReplacement|More...]]
 |-
@@ Line 96: / Line 115: @@
 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...]]

@@ Line 42: / Line 42: @@
 == [[Algorithm:MGH:NRDDFreesurfer|Adding NRRD I/O to Freesurfer]] ==
 |-
@@ Line 66: / Line 67: @@
 == [[Algorithm:MGH:QBALLVisualization|QBall Visualization]] ==
 |-

@@ Line 40: / Line 40: @@
 == [[Engineering:Project:Non-rigid_EPI_registration|Engineering:Project:Non-rigid_EPI_registration]] ==
-* '''Use case'''<nowiki>: 'Evaluate benefit of using ITK nonlinear registration for group FA comparisons' </nowiki>
+My objective is to evaluate the benefit of using ITK nonlinear registration for group FA comparisons. [[Engineering:Project:Non-rigid_EPI_registration|More...]]
 |-
@@ Line 52: / Line 49: @@
 == [[Algorithm:MGH:NRDDFreesurfer|Adding NRRD I/O to Freesurfer]] ==
 |-
@@ Line 88: / Line 74: @@
 == [[Algorithm:MGH:QBALLVisualization|QBall Visualization]] ==
 |-
@@ Line 107: / Line 82: @@
 == [[Algorithm:MGH:Development:GroupComp|Tensor-based group comparison (Cramer test)]] ==
-* '''Use case'''<nowiki>: 'Compare DTI images between groups using the full tensor information.' </nowiki>
+Our objective is to boost statistical sensitivity for group comparisons in comparison to 'traditional' univariate tests. [[Algorithm:MGH:Development:GroupComp|More...]]
 |-
@@ Line 126: / Line 90: @@
 == [[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...]]
 |-
@@ Line 144: / Line 100: @@
 == [[Algorithm:MGH:Development:AutoBrainSeg|Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms]] ==
-* '''Use Case'''<nowiki>: 'Atlas-based fully automated whole brain segmentation' </nowiki>
+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...]]

@@ Line 87: / Line 87: @@
 | |
-== QBALL visualization ==
+== [[Algorithm:MGH:QBALLVisualization|QBall Visualization]] ==
 * '''Use case'''<nowiki>: 'Visualize q-ball data in Slicer.' </nowiki>

@@ Line 11: / Line 11: @@
 | style="width:90%" |
-== QDEC: An easy to use GUI for group morphometry studies ==
+== [[Algorithm:MGH:QDEC|QDEC: An easy to use GUI for group morphometry studies]] ==
 * Difficulty: Medium
@@ Line 33: / Line 33: @@
 * Difficulty: High
 * Impact: High
 == [[Engineering:Project:Non-rigid_EPI_registration|Engineering:Project:Non-rigid_EPI_registration]] ==
@@ Line 46: / Line 51: @@
 | |
-== Adding NRRD I/O to Freesurfer ==
+== [[Algorithm:MGH:NRDDFreesurfer|Adding NRRD I/O to Freesurfer]] ==
 * '''Use case'''<nowiki>: 'Open a NRRD volume in FreeSurfer.' </nowiki>