DBP2:MIND:Roadmap - Revision history

Mscully: /* Team and Institute */

2011-01-18T17:09:45Z

Team and Institute

2010-06-10T15:27:52Z

Roadmap

2010-05-24T14:44:40Z

Incorporated the zoomed image into the table

2010-05-21T13:36:10Z

Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus

2010-05-13T18:18:46Z

Software

2010-05-13T18:03:31Z

Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus: Changed volume image

2010-05-13T17:52:32Z

Roadmap: Changed compare layout zoomed-in image

2010-05-13T17:48:36Z

Roadmap: Changed compare layout overview image

2010-05-13T17:16:29Z

Roadmap: Updated segmented image caption

2010-05-12T17:13:54Z

Schedule

@@ Line 85: / Line 85: @@
 * Co-PI: [http://www.mrn.org/principal-investigators/h-jeremy-bockholt H Jeremy Bockholt]  (jbockholt at mrn.org)
 * Co-PI: [http://www.mrn.org/principal-investigators/charles-gasparovic-ph-d Charles Gasparovic] (chuck at unm.edu)
-* Software Engineer: Mark Scully (mscully at mrn.org)
+* Software Engineer: Mark Scully (mark-scully at uiowa.edu)
 * NA-MIC Engineering Contact: [http://www.na-mic.org/Wiki/index.php/User:Pieper Steve Pieper], Isomics
 * NA-MIC Algorithms Contact: Ross Whitaker, Utah

@@ Line 20: / Line 20: @@
 {|
 |[[Image:Scully Figure3.jpg|thumb|400px|A. FLAIR with predicted probability of being lesion, B. FLAIR with manual segmentation, C. FLAIR with predicted probability after thresholding]]
-|[[Image:TractsLesionZoomOverlay.png‎|thumb|380px|White Matter Lesion Track Disruption]]
+|[[Image:TractsLesionZoomOverlay.png‎|thumb|380px|White Matter Lesion Disruption of a U fiber]]
 |}
 {|

@@ Line 25: / Line 25: @@
 |[[Image:ComapareViewL1L2Overview.jpg|thumb|400px| Compare Layout overview with baseline FLAIR image on top and followup FLAIR on bottom.  Each image is overlaid with that time point's predicted lesion segmentation.]]
 |[[Image:CompareViewLDiffZoomedIn.jpg|thumb|400px| Compare Layout zoomed in.  Baseline FLAIR on top and followup on bottom.  Images overlaid with a label map that represents changes in lesion.  Yellow represents lesion that's unchanged between baseline and followup, red represents new lesion in the followup, and blue represents lesion present at baseline that is no longer present at followup. ]]
 |}
 </center>
 ===Software===

@@ Line 27: / Line 27: @@
 |}
 </center>
 ===Software===

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 ===Software===
 *We have a very active project for this pipeline on the NITRC resource [http://www.nitrc.org/frs/?group_id=180 3DSlicerLupusLesionModule]
-** The module can be checked out in Slicer3.6 using the extension manager or downloaded [http://www.nitrc.org/frs/download.php/570/LesionSegmentationApplications.tgz here].
+*The module can be checked out in Slicer3.6 using the extension manager or downloaded [http://www.nitrc.org/frs/download.php/570/LesionSegmentationApplications.tgz here].
-** Source code is available via [http://www.nitrc.org/plugins/scmcvs/cvsweb.php/lupuslesion/LesionSegmentationApplications/?cvsroot=lupuslesion cvs].
+*Source code is available via [http://www.nitrc.org/plugins/scmcvs/cvsweb.php/lupuslesion/LesionSegmentationApplications/?cvsroot=lupuslesion cvs].
 === Tutorial ===

@@ Line 3: / Line 3: @@
 =Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus=
-[[Image:LesionInBrain-PW2009.png‎|thumb|280px|Lesion Model inside Brain]]
+[[Image:BrainVentriclesAndLesions.png‎|thumb|280px|Lesion volumes in yellow with ventricles and brain slice]]
 =='''Objective'''==
 This page describes the technology roadmap for lesion analysis in the NA-MIC Kit. Our objective is to create an end-to-end application allowing individual analysis of white matter lesions. This workflow applied to lupus patients is one of goals of the [[DBP2:MIND:Introduction|MIND DBP]].  The basic components necessary for this project are:

@@ Line 23: / Line 23: @@
 |}
 {|
-|[[Image:CompareViewFlairLesionDiffWholeBrain.png|thumb|333px| Whole brain compare view of FLAIR with longitudinal lesion changes]]
+|[[Image:ComapareViewL1L2Overview.jpg|thumb|400px| Compare Layout overview with baseline FLAIR image on top and follow-up FLAIR on bottom.  Each image is overlaid with that time point's predicted lesion segmentation.]]
-|[[Image:CompareViewFlairLesionDiff.png|thumb|333px| Longitudinal compare view zoomed in]]
+|[[Image:CompareViewFlairLesionDiff.png|thumb|400px| Longitudinal compare view zoomed in]]
 |}
 </center>

@@ Line 19: / Line 19: @@
 <center>
 {|
-|[[Image:Scully Figure3.jpg|thumb|400px|Predicted Heat Map, Manual Segmentation, Thresholded Heat Map]]
+|[[Image:Scully Figure3.jpg|thumb|400px|A. FLAIR with predicted probability of being lesion, B. FLAIR with manual segmentation, C. FLAIR with predicted probability after thresholding]]
 |[[Image:TractsLesionZoomOverlay.png‎|thumb|380px|White Matter Lesion Track Disruption]]
 |}

@@ Line 37: / Line 37: @@
 * The data needed to run the tutorial is available [http://www.nitrc.org/frs/download.php/569/LesionSegmentationTutorialData.tgz here].
-=== '''Schedule''' ===
+=== Schedule ===
 * 06/25/2007 - 06/29/2007 Attended Project Week
 === '''Publications''' ===