Page History

Analysis Mask Files DescriptionMRI Studies

Trial time points for MRI studies

...

1. Single-breast ipsilateral cropped DCE images
   1. As this was done primarily for computational efficiency, low matrix-sized images (<384 voxels per row) were stored and processed without cropping
2. Enhancement maps
   1. PE_early: Enhancement at effective post-contrast time 120-150 sec
   2. PE_late: Enhancement at effective post-contrast time ~450 sec
   3. SER: Signal enhancement ratio    SER =  PE_early / PE_late
      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.
   4. All maps were stored as DICOM MRI objects
3. Functional Tumor Volume (FTV) analysis mask
   1. Segmentation storing FTV masking. Encodes:
      1. Pre-contrast background threshold
      2. Minimum PE threshold (70% nom.)
      3. Manually defined rectangular volume of interest (VOI) for enhancing tumor analysis
      4. Manually defined “OMIT” regions used to exclude non-tumor enhancing regions that encroached on the rectangular VOI
   2. Stored as DICOM SEG object
   3. See this document for further information: <Analysis mask files description.docx> Analysis Mask Files Description

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.

...

1. 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 1^st and 2^nd scans respectively.
2. 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.
3. 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.

...

• 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>

...

• 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 ]]]
  
  

...