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)