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MR imaging was performed on a 1.5 or 3.0 Tesla scanner using a dedicated breast radiofrequency coil. All studies for a given patient were required to be performed on the same scanner configuration (model, field strength and breast coil model). Subjects were imaged in the prone position. The image acquisition protocol included a localization scan and a minimum of three required acquisitions:
- T2-weighted sequence
- DWI (b=0, 100, 600, 800 s/mm2, 3-direction)
- T1-weighted DCE (80sec < phase duration < 100sec; > 8 minutes continuous post-injection acquisition)
Protocol limits on scan parameters for these required acquisitions are given in an accompanying document (see final section on this page).: NEED LINK ACRIN-6698 MRI Acquisition Parameters
All required imaging was performed axially with full bilaterally coverage. For the TCIA collection all original images from these three acquisitions are included. Derived images including reformats, CAD software outputs and MIP images are not part of the collection. For the T2wT2weighted acquisitions multiple series are included if they were generated as part of the standard reconstruction process on the scanner. For example, acquisitions utilizing Dixon techniques to create separate fat and water images will have multiple series in the collection. All original DWI series are includedDW images are in the collection, including directional diffusion images if they were stored with the study. For some General Electric Medical systems (GEMS) scanners employed in the trial the acquisition software allowed only 2 b-values in a single DWI acquisition. For studies on these scanners the multiple b-value protocol DWI consisted of three consecutive two b-value series (b = [0,800], [0,600] and [0,100] s/mm2). A separate “merged series multi-b” (MSMB) series containing all b>0 images from the three series plus a single b=0 s/mm2 image created by averaging the three acquired b=0 images was created for analysis and is included in the collection. The DICOM metadata fields in the MSMB series have been set to permit reading as a standard GEMS multi-b acquisition. During automated QC procedures, the MSMB series were rejected if any sequence related parameters other than the b value differed between the multiple two b-value acquisitions. The original 2-b acquisition series are also included in the collection.
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Derived objects from the DWI and DCE acquisitions are included for the convenience of the user. Some of these are not strictly DICOM compliant and may not be readable by all DICOM software packages. Parametric maps and segmentations are believed to be identical to those utilized in the primary analysis and test/retest repeatability analyses of the 6698 Trial, but in isolated some cases modifications may have occurred in subsequent processing.
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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 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, identical to the original DCE images except for the changed series ID and description fields.
DICOM Dictionary for UCSF Private Attributes in Derived Objects:
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While every effort was made to preserve the integrity of both the original image data and image meta-data (DICOM attributes, public and private), multiple file transfers and strict adherence to HIPAA guidelines for patient confidentiality may have resulted in loss of some data. If any questions arise, or if any patient PHI is found in any data on this collection, please contact the UCSF Breast Imaging Research Program (BIRP). UCSF I-SPY 2 Imaging Lab
Ancillary files for the ACRIN-6698 collection
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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.
BMMR2 Challenge case list: Training set : QINChallenge_CaselistTrain_20210108wClinicalData
Test set; QINChallenge_CaselistTest_20210108wClinicalData
Test/ReTest set: <ACRIN_6698_n71TestReTest_wClinicalData.csv>with clinical data
BMMR2 Challenge case list: Test set with clinical data
NEED LINK ACRIN-6698 71 patient test/retest case list with clinical data - 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
NEED LINK ACRIN-6698 MRI Acquisition Parameters - 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 - DICOM Dictionary for UCSF private attributes
[[[XXX need to finalize ]]]and data descriptions for UCSF derived objects (Excel and pdf files)
NEED LINK UCSF Shared Private Tag Data Dictionary
NEED LINK DWI+DCE UCSF Derived Object Descriptions