Analysis Mask Files DescriptionMRI Studies
Trial time points for MRI studies
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- Single-breast ipsilateral cropped DCE images
- As this was done primarily for computational efficiency, low matrix-sized images (<384 voxels per row) were stored and processed without cropping
- Enhancement maps
- PEearly: Enhancement at effective post-contrast time 120-150 sec
- PElate: Enhancement at effective post-contrast time ~450 sec
- SER: Signal enhancement ratio SER = PEearly / PElate
Note: SER values were scaled by 1000 for integer storage. DICOM software utilizing the rescale slope and intercept fields [ DICOM fields (0028, 1052-1054)] should return the original SER values in the range from 0.0 – 3.0. - All maps were stored as DICOM MRI objects
- Functional Tumor Volume (FTV) analysis mask
- Segmentation storing FTV masking. Encodes:
- Pre-contrast background threshold
- Minimum PE threshold (70% nom.)
- Manually defined rectangular volume of interest (VOI) for enhancing tumor analysis
- Manually defined “OMIT” regions used to exclude non-tumor enhancing regions that encroached on the rectangular VOI
- Stored as DICOM SEG object
- See this document for further information: <Analysis mask files description.docx> Analysis Mask Files Description
- Segmentation storing FTV masking. Encodes:
These DCE derived series can be identified either by Series Description (0008,103e) or by Series Number (0020,0011). See Table 1 for series identification details.
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- For studies with test/retest DWI scans the prefixes on the series descriptions for the derived DWI objects will be “ACRIN-6698: TrT0:” and “ACRIN-6698: TrT1” for the 1st and 2nd scans respectively.
- FTV (functional tumor volume) Analysis Masks are bit-encoded segmentations encoding all masking steps in the I‑SPY 2 primary FTV analysis. See document [<Analysis mask files description.docx> link] Analysis Mask Files Description for a full description of these objects.
- DCE images with less than 384 voxels/row were not cropped for the FTV analysis. For these studies the derived DCE objects are all full bilateral images.
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- BMMR2 Challenge patient demographic, clinical and outcome data files for the training and test cohorts (comma-separated text files).
Due to the ongoing nature of the I‑SPY 2 Trial only this limited set of patient data can be released at this time. Further information will become available with release of further I‑SPY 2 imaging data.
Training set: QINChallenge_CaselistTrain_20210108wClinicalData
Test set; QINChallenge_CaselistTest_20210108wClinicalData - Full collection ancillary patient information file (comma-separated text file). Includes clinical and outcome data, DWI Quality Control ratings, and cohort identification.
This file will be made available at the conclusion of the BMMR2
<ACRIN_6698_Patient_Cohorts_ClinicalData.csv>
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- ACRIN 6698 MRI protocol parameter specifications
- DCE analysis mask description. This file provides usage information for the functional tumor volume analysis masks provided as part of the DCE derived objects package
<Analysis mask files description.docx>Analysis Mask Files Description - DICOM Dictionary for UCSF private attributes
[[[XXX need to finalize ]]]
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