Slicer3:UIDesign:WorkingProblems:BCAnalysis:Dynamic - Revision history

Wjp: /* Pre-treatment VOI defined as guided by functional imaging analysis slide from JHU */

2009-09-14T15:44:25Z

Pre-treatment VOI defined as guided by functional imaging analysis slide from JHU

Wjp: /* First experiment */

2009-09-14T15:42:39Z

First experiment

Wjp: /* First experiment */

2009-09-14T15:41:51Z

First experiment

Wjp: /* NUMPY for Slicer and python2.5 on win32 */

2009-09-14T15:41:08Z

NUMPY for Slicer and python2.5 on win32

Wjp: /* Goal */

2009-09-14T15:19:15Z

Goal

Wjp at 12:18, 14 September 2009

2009-09-14T12:18:19Z

Wjp: /* Experiments to define best VOI */

2009-09-02T20:06:01Z

Experiments to define best VOI

Wjp: /* Experiments to define best VOI */

2009-09-02T13:18:12Z

Experiments to define best VOI

Wjp: /* Experiments to define best VOI */

2009-09-02T13:16:49Z

Experiments to define best VOI

Wjp: /* Experiments to define best VOI */

2009-09-02T13:16:14Z

Experiments to define best VOI

@@ Line 136: / Line 136: @@
 [[image:CaseComparisonJHU.png|thumb|center|400px|Pre/Post comparison slide from JHU.]]
-[[image:PreTreatmentPerfusionPlotSmallVOI.png|thumb|center|400px| Several plots for similar VOI.]]
+[[image:PreTreatmentPerfusionPlotSmallVOI.png|thumb|center|400px| Plot for similar VOI, no threshold.]]
 === Pre-treatment VOI defined with strict intensity threshold (>1100) ===

@@ Line 119: / Line 119: @@
 ** for curve fitting, specify the color of the tumor label.
-Not reliable scipy install on win32. module functions thru plotting, but curve fitting not working.
+Not reliable scipy install on win32. module functions thru plotting, but curve fitting still not working cross-platform (only Mac).
 == Experiments to define best VOI ==

@@ Line 102: / Line 102: @@
 * Save scene PreTreatmentPerfusion.mrml
 * Reload & see if volumeBundleNode reloads properly.
-** BUG: looks like timeseries bundles did not get saved; FourDAnalysis module requires user to select a timeseries Bundle for plotting; none exists in the reloaded scene. Looks like FourDImage contains methods to serialize the mrml node, so maybe save was not good. Try again.
+** BUG: looks like timeseries bundles did not get saved; FourDAnalysis module requires user to select a timeseries Bundle for plotting; none exists in the reloaded scene. Looks like FourDImage contains methods to serialize the mrml node, so maybe save was not good.
-**
+** Yes, BUG FIXED.
 * Segment tumor & bloodpool
 ** in editor, select either Volname_Display0 or Volname_Display1 as src volume for label map -- Select Volname_Display1 (some label map out of range error occurs with Volname_Display0 for some reason... or maybe it's just an error enocuntered for the first label map created. don't know)

← Older revision		Revision as of 15:41, 14 September 2009
Line 94:		Line 94:

	Started slicer, opened python console, typed import numpy and import scipy and seemed to get the right behavior.		Started slicer, opened python console, typed import numpy and import scipy and seemed to get the right behavior.
		+
		+	==== >>>>>>> SHOULD NOT RELY ON SCIPY FOR BROAD USE: IMPLEMENT IN C++====

	== First experiment ==		== First experiment ==

@@ Line 5: / Line 5: @@
 == Goal==
-Goal is to accommodate basic RECIST assessment for breast cancer (Response Evaluation Criteria In Solid Tumors). (RECIST is a set of published rules that define when cancer patients improve ("respond"), stay the same ("stable") or worsen ("progression") during treatments).
+Goal is to accommodate basic RECIST assessment for cancer treatment.
-* Determine features that currently exist in Slicer
+Specifically for Perfusion analysis: Develop a module that loads perfusion datasets and performs fits intensity timecourse data to Tofts Kinetic Model.
 == Perfusion Analysis Workflow ==

← Older revision		Revision as of 12:18, 14 September 2009
Line 156:		Line 156:

	[[image:MaskedThresholdAbove1100PlotPlusMaskAndAIF.png\|thumb\|center\|400px\| Same as above with all intensities inside tumor and with bloodpool thresholded to include intensities > 350. ]]		[[image:MaskedThresholdAbove1100PlotPlusMaskAndAIF.png\|thumb\|center\|400px\| Same as above with all intensities inside tumor and with bloodpool thresholded to include intensities > 350. ]]
		+
		+	== Approach & STATUS ==
		+	* Need to compute VOI for tumor necrotic region and confirm flat plot
		+	* Current status:
		+	** FourDImage module not exposed to users in release or nightlies
		+	** Only available in developer builds
		+	** Need to refine and expose by November (RSNA deadline)
		+	** FourDAnalysis module which implements Tofts Kinetic Model for curve fitting uses specialized components
		+	*** (scipy) doesn't build/install on all Slicer platforms
		+	*** (scipy) requires lots of hand-holding to install properly
		+	*** must convert module to C++ for cross-platform build (November deadline?)
		+	** Need to implement idealized arterial input function if no AIF available in dataset (November deadline?)
		+
		+	== PPT Slides ==
		+
		+	[[media:PerfusionPresentation.ppt \| Slides for Perfusion Presentation]]

← Older revision		Revision as of 20:06, 2 September 2009
Line 140:		Line 140:
	=== Pre-treatment VOI defined with strict intensity threshold (>1100) ===		=== Pre-treatment VOI defined with strict intensity threshold (>1100) ===
	[[image:PreTreatmentPerfusionVOIThreshOver1100.png\|thumb\|center\|400px\|VOI defined with thres paint.]]		[[image:PreTreatmentPerfusionVOIThreshOver1100.png\|thumb\|center\|400px\|VOI defined with thres paint.]]
		+
		+	=== Pre-treatment VOI defined with various intensity threshold & mask ===
		+
		+	Thresholding to define 3 VOIs:
		+	* 600 to max
		+	* 950 to max
		+	* 1100 to max
		+	Masked each image with the segmentation of tumor to cull any voxels outside.
		+
		+	[[image:MaskedThresholdAbove600Plot.png\|thumb\|center\|400px\| Thresholded out tumor intensities < 600. ]]
		+
		+	[[image:MaskedThresholdAbove950Plot.png\|thumb\|center\|400px\| Thresholded out tumor intensities < 950. ]]
		+
		+	[[image:MaskedThresholdAbove1100Plot.png\|thumb\|center\|400px\| Thresholded out tumor intensities < 1100. ]]
		+
		+	[[image:MaskedThresholdAbove1100PlotPlusMaskAndAIF.png\|thumb\|center\|400px\| Same as above with all intensities inside tumor and with bloodpool thresholded to include intensities > 350. ]]

@@ Line 125: / Line 125: @@
 === Pre-treatment VOI defined by careful tumor segmentation ===
-[[image:PreTreatmentPerfusionPlots.png|thumb|400px|Pre-TX. ]]
+[[image:PreTreatmentPerfusionPlots.png|thumb|center|400px|Pre-TX. ]]
-[[image:PostTreatmentPerfusionPlots.png|thumb|400px|Post-TX.]]
+[[image:PostTreatmentPerfusionPlots.png|thumb|center|400px|Post-TX.]]
 Post-treatment scan appears to use different acquisition params from Pre-TX study. Suggested that Post-TX scan may not have used fat suppression. One suggestion is to carefully define VOI in Post-TX to include only scar, and to exclude anything that might look like fat. (will this not also potentially exclude tumor tissue?) Error bars too huge on Pre-Tx scan -- the analysis is weak. Try to exclude what we know to be necrotic tissue within the tumor.
@@ Line 134: / Line 134: @@
 Using the following image provided by JHU to define a small VOI within Pre-TX tumor:
-[[image:CaseComparisonJHU.png|thumb|400px|Pre/Post comparison slide from JHU.]]
+[[image:CaseComparisonJHU.png|thumb|center|400px|Pre/Post comparison slide from JHU.]]
-[[image:PreTreatmentPerfusionPlotSmallVOI.png|thumb|400px| Several plots for similar VOI.]]
+[[image:PreTreatmentPerfusionPlotSmallVOI.png|thumb|center|400px| Several plots for similar VOI.]]
 === Pre-treatment VOI defined with strict intensity threshold (>1100) ===
-[[image:PreTreatmentPerfusionVOIThreshOver1100.png|thumb|400px|VOI defined with thres paint.]]
+[[image:PreTreatmentPerfusionVOIThreshOver1100.png|thumb|center|400px|VOI defined with thres paint.]]

@@ Line 125: / Line 125: @@
 === Pre-treatment VOI defined by careful tumor segmentation ===
-[[image:PreTreatmentPerfusionPlots.png ]]
+[[image:PreTreatmentPerfusionPlots.png|thumb|left|400px|Pre-TX. ]]
-[[image:PostTreatmentPerfusionPlots.png ]]
+[[image:PostTreatmentPerfusionPlots.png|thumb|left|400px|Post-TX.]]
 Post-treatment scan appears to use different acquisition params from Pre-TX study. Suggested that Post-TX scan may not have used fat suppression. One suggestion is to carefully define VOI in Post-TX to include only scar, and to exclude anything that might look like fat. (will this not also potentially exclude tumor tissue?) Error bars too huge on Pre-Tx scan -- the analysis is weak. Try to exclude what we know to be necrotic tissue within the tumor.
@@ Line 134: / Line 134: @@
 Using the following image provided by JHU to define a small VOI within Pre-TX tumor:
-[[image:CaseComparisonJHU.png]]
+[[image:CaseComparisonJHU.png|thumb|left|400px|Pre/Post comparison slide from JHU.]]
-[[image:PreTreatmentPerfusionPlotSmallVOI.png ]]
+[[image:PreTreatmentPerfusionPlotSmallVOI.png|thumb|left|400px| Several plots for similar VOI.]]
 === Pre-treatment VOI defined with strict intensity threshold (>1100) ===
-[[image:PreTreatmentPerfusionVOIThreshOver1100.png ]]
+[[image:PreTreatmentPerfusionVOIThreshOver1100.png|thumb|left|400px|VOI defined with thres paint.]]