Difference between revisions of "Slicer3:UIDesign:WorkingProblems:BCAnalysis:Volumetric"

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== Goal==
 
== 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 volumetric analysis:
* Develop features that don't
+
* perform linear measurements
* Provide a framework that knits features together in a comfortable workflow.
+
* perform volumetric measurements
 +
* test change tracker in cases where linear measurements may not provide clear assessment.
  
== Linear Measurements Workflow ==
+
== Linear Measurements Workflow Described by Jeffrey Yapp ==
  
 
* Scroll through baseline
 
* Scroll through baseline
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** Percent change
 
** Percent change
 
** Absolute change  
 
** Absolute change  
** '''Question:''' units for these values -- mm^2?
+
** '''Question:''' units for these values -- mm!
 +
 
 +
== Approach in Slicer ==
 +
 
 +
* create a subvolume of target breast for both pre and post treatment timepoints: try to make these two subvolumes match as closely as possible. Ron uses 2-fold oversampling.
 +
* Registration:
 +
** create transform node
 +
** perform manual,
 +
** then affine,
 +
** then B-spline (modified number of histogram bins to 20)
 +
* run bias field correction on both subvolumes with 10 iterations and skin mask for pre and post separately
 +
* mask out background
 +
* perform histogram matching with "threshold at mean" checked
 +
* Ran diffeomorphic demons on post, took 3 hours, with nice results
 +
* Linear Measurements:
 +
** scroll to slice with largest diameter Dmax
 +
** measure Dmax and orthogonal Dmax on both treatment timepoints using the linear measurement widget.
 +
* in Editor module:
 +
** use threshold paint to segment tumor; or
 +
** use fastmarching with seeds in the tumor tissue
 +
** erase any outlying pixels
 +
* in Fiducials module:
 +
** create two fiducials along longest axis
 +
** check distance measure between; or
 +
** eventually use nicole's measurement widget
 +
** move fiducials to mark orthogonal axis
 +
** check distance measure between;
 +
* Extra things to do:
 +
** use the editor quick model to create a model of the gland
 +
** use the editor to segment the skin (threshold, change island, quick model)
 +
 
 +
Ron's requests:
 +
 
 +
* The fiducial text is too large in the fast marching display. The default text size be smaller?
 +
* I was not quite clear on how to create a new label map for doing the skin segmentation. I ended up reusing the fastmarchinglabel and losing that segmentation.
 +
* quickmodel should use the label name as default.
 +
* It would be nice to have short cuts to the add label tools and label statistics tools on the editor page. This would give a cue for beginners where to look for that functionality.
  
 
== Volume Measurements Workflow ==
 
== Volume Measurements Workflow ==
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* Segment largest diameter tumor in baseline '''Question:''' multiple tumors ok?
 
* Segment largest diameter tumor in baseline '''Question:''' multiple tumors ok?
 
** Manual or automatic segmentation OK
 
** Manual or automatic segmentation OK
* Segment tumor in followup '''Questions:''' Must be same tumor, or largest diameter in followup? multiple tumors ok?
+
* Segment tumor in followup '''Questions:''' Must be same tumor, or largest diameter in followup? multiple tumors ok? (same tumor)
 
** Manual or automatic segmentation OK -- but use same method
 
** Manual or automatic segmentation OK -- but use same method
 
* Measure:
 
* Measure:
** Volume(t1) and Volume(t2) '''Question:''' which is preferred, mm^3 or cc?
+
** Volume(t1) and Volume(t2) '''Question:''' which is preferred, mm^3!
 
** Relative % difference
 
** Relative % difference
 
** Absolute change (same units as above)
 
** Absolute change (same units as above)
 +
 +
== Screenshots ==
 +
 +
=== Linear Measurement (from draft slides) ===
 +
 +
[[image:PreTreatmentLinear1.png |thumb|center|400px| measuring pre-TX tumor with fiducials, longest dimension]]
 +
 +
[[image:PreTreatmentLinear1cross.png |thumb|center|400px| measuring pre-TX tumor with fiducials, orthogonal dimension]]
 +
 +
[[image:PreTreatmentNewWidget.png |thumb|center|400px| measuring pre-TX tumor with MeasureWidget, orthogonal dimension]]
 +
 +
[[image:PostTreatmentLinear1.png |thumb|center|400px| measuring pre-TX tumor with fiducials, longest dimension]]
 +
 +
[[image:PostTreatmentLinear1cross.png |thumb|center|400px| measuring pre-TX tumor with fiducials, orthogonal dimension]]
 +
 +
=== Volumetric Measurement (from draft slides) ===
 +
 +
[[image:CreateVOI.png |thumb|center|400px| defining VOI for measurements]]
 +
 +
[[image:PreTreatmentVolumeStats.png |thumb|center|400px| pre-TX statistics]]
 +
 +
[[image:PostTreatmentVolumeStats.png |thumb|center|400px| post-TX statistics]]
 +
 +
[[image:CompareVolumeStatistics.png |thumb|center|400px| pre- versus post-TX statistics]]
 +
 +
== STATUS ==
 +
 +
* have new Pre/Post GAD Ax case for post-treatment -- need to regenerate slides and workflow with this dataset instead of T1 for better tumor contrast (November RSNA deadline)
 +
* need to use dataset appropriate for ChangeTracker demonstration -- t2 for this dataset has no detectable tumor (November RSNA deadline)
 +
 +
== PPT files ==
 +
 +
[[media:VolumetricPresentation.ppt | Slides for Volumetric Analysis (in progress) ]]

Latest revision as of 15:38, 14 September 2009

Home < Slicer3:UIDesign:WorkingProblems:BCAnalysis:Volumetric

Back to Project Overview

Volumetric Tumor Analysis for Breast Cancer

Goal

Goal is to accommodate basic RECIST assessment for cancer treatment.

Specifically for volumetric analysis:

  • perform linear measurements
  • perform volumetric measurements
  • test change tracker in cases where linear measurements may not provide clear assessment.

Linear Measurements Workflow Described by Jeffrey Yapp

  • Scroll through baseline
  • Find the tumor's longest diameter (no reformat, just on orig acquisition)
  • Measure the longest diameter D1(t1)
  • Measure the orthogonal diameter D2(t1)
  • If there are multiple tumors, measure both diams in each tumor and sum to get relative D1(t1) and relative D2(t1)
  • Perform same measurements D1(t2) and D2(t2)
  • Specific results to report:
    • Percent change
    • Absolute change
    • Question: units for these values -- mm!

Approach in Slicer

  • create a subvolume of target breast for both pre and post treatment timepoints: try to make these two subvolumes match as closely as possible. Ron uses 2-fold oversampling.
  • Registration:
    • create transform node
    • perform manual,
    • then affine,
    • then B-spline (modified number of histogram bins to 20)
  • run bias field correction on both subvolumes with 10 iterations and skin mask for pre and post separately
  • mask out background
  • perform histogram matching with "threshold at mean" checked
  • Ran diffeomorphic demons on post, took 3 hours, with nice results
  • Linear Measurements:
    • scroll to slice with largest diameter Dmax
    • measure Dmax and orthogonal Dmax on both treatment timepoints using the linear measurement widget.
  • in Editor module:
    • use threshold paint to segment tumor; or
    • use fastmarching with seeds in the tumor tissue
    • erase any outlying pixels
  • in Fiducials module:
    • create two fiducials along longest axis
    • check distance measure between; or
    • eventually use nicole's measurement widget
    • move fiducials to mark orthogonal axis
    • check distance measure between;
  • Extra things to do:
    • use the editor quick model to create a model of the gland
    • use the editor to segment the skin (threshold, change island, quick model)

Ron's requests:

  • The fiducial text is too large in the fast marching display. The default text size be smaller?
  • I was not quite clear on how to create a new label map for doing the skin segmentation. I ended up reusing the fastmarchinglabel and losing that segmentation.
  • quickmodel should use the label name as default.
  • It would be nice to have short cuts to the add label tools and label statistics tools on the editor page. This would give a cue for beginners where to look for that functionality.

Volume Measurements Workflow

  • Scroll through dataset and determine tumor with largest diameter.
  • Segment largest diameter tumor in baseline Question: multiple tumors ok?
    • Manual or automatic segmentation OK
  • Segment tumor in followup Questions: Must be same tumor, or largest diameter in followup? multiple tumors ok? (same tumor)
    • Manual or automatic segmentation OK -- but use same method
  • Measure:
    • Volume(t1) and Volume(t2) Question: which is preferred, mm^3!
    • Relative % difference
    • Absolute change (same units as above)

Screenshots

Linear Measurement (from draft slides)

measuring pre-TX tumor with fiducials, longest dimension
measuring pre-TX tumor with fiducials, orthogonal dimension
measuring pre-TX tumor with MeasureWidget, orthogonal dimension
measuring pre-TX tumor with fiducials, longest dimension
measuring pre-TX tumor with fiducials, orthogonal dimension

Volumetric Measurement (from draft slides)

defining VOI for measurements
pre-TX statistics
post-TX statistics
pre- versus post-TX statistics

STATUS

  • have new Pre/Post GAD Ax case for post-treatment -- need to regenerate slides and workflow with this dataset instead of T1 for better tumor contrast (November RSNA deadline)
  • need to use dataset appropriate for ChangeTracker demonstration -- t2 for this dataset has no detectable tumor (November RSNA deadline)

PPT files

Slides for Volumetric Analysis (in progress)