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- 1 Volumetric Tumor Analysis for Breast Cancer
Volumetric Tumor Analysis for Breast Cancer
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.
- 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)
- 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
- Volume(t1) and Volume(t2) Question: which is preferred, mm^3!
- Relative % difference
- Absolute change (same units as above)
Linear Measurement (from draft slides)
Volumetric Measurement (from draft slides)
- 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)