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

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== Approach in Slicer ==
 
== Approach in Slicer ==
* create a subvolume of target breast
+
* create a subvolume of target breast for both timepoints: try to make these two subvolumes match as closely as possible.
 +
* run bias field correction on both subvolumes
 +
* mask out background
 +
* perform histogram matching (normalization across both subvolumes)
 +
* registration
 +
** create transform node
 +
** put moving volume under transform
 +
** manually transform to get close
 +
** perform non-linear transform
 +
** perform nonlinear transform (bspline?) ?
 +
** resample (or do we have to resample prior to bspline xform?)
 +
* Linear Measurements:
 +
** scroll to slice with largest diameter Dmax
 +
** measure Dmax on both timepoints, and orthogonal Dmax using the linear measurement widget.
 
* in Editor module:
 
* in Editor module:
** choose subvolume
 
** scroll to slice with largest diameter
 
 
** use threshold paint to segment tumor; or
 
** use threshold paint to segment tumor; or
 
** use fastmarching with seeds in the tumor tissue
 
** use fastmarching with seeds in the tumor tissue

Revision as of 16:40, 20 August 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 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).

  • Determine features that currently exist in Slicer
  • Develop features that don't
  • Provide a framework that knits features together in a comfortable workflow.

Linear Measurements Workflow

  • 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 timepoints: try to make these two subvolumes match as closely as possible.
  • run bias field correction on both subvolumes
  • mask out background
  • perform histogram matching (normalization across both subvolumes)
  • registration
    • create transform node
    • put moving volume under transform
    • manually transform to get close
    • perform non-linear transform
    • perform nonlinear transform (bspline?) ?
    • resample (or do we have to resample prior to bspline xform?)
  • Linear Measurements:
    • scroll to slice with largest diameter Dmax
    • measure Dmax on both timepoints, and orthogonal Dmax 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)