MRI Studies

Trial time points for MRI studies

MRI studies were performed at up to four time points in the course of NAC:

1. Pre-treatment (T0, optional test/retest visit)
   Prior to randomization patients received an MRI study including T2_weighted, DWI, and dynamic contrast-enhanced (DCE) acquisitions.

For patients randomized onto a treatment or control arm of I‑SPY 2 subsequent MRI studies with the same required acquisitions were performed:

1. Early-treatment (T1, optional test/retest visit)
   After 3 weeks of regimen 1 treatment (Paclitaxel with or without an experimental agent).
2. Mid-treatment (T2)
   Between Paclitaxel and Anthracycline (AC) treatment regimens
3. Post-treatment (T3)
   Following 4 cycles AC and prior to surgery.

Figure 1. I-SPY 2 study schema.

Imaging protocol and included original image series

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 two acquisitions:

1. T2_weighted sequence
2. T1_weighted DCE (80sec < phase duration < 100sec with at least 8 minutes continuous post-injection acquisition)

The DWI acquisitions (b=0, 100, 600, 800 s/mm² OR b=0, 800) were also acquired but are undergoing quality review and are not included in the collection at this time.

Protocol limits on scan parameters for these required acquisitions are given in an accompanying document

All required imaging was performed axially with full bilaterally coverage. For the TCIA collection all original images from the two acquisitions are included. Derived images submitted with the study including reformats, CAD software outputs and MIP images are not part of the collection. For the T2_weighted 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 T2_weighted series in the collection.

Derived object series:

Derived objects from the 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 analyses of the I-SPY 2 Trial, but in some cases modifications may have occurred in subsequent processing.

DCE “Package” for each study

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. All maps and segmentations are based on these cropped images
2. Enhancement maps
   1. PE_early: Percent enhancement at effective post-contrast time 120-150 sec
   2. PE_late: Percent 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 to allow 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 are stored as DICOM MRI objects
3. Functional Tumor Volume (FTV) analysis mask
   1. Image storing FTV masking processes on a pixel-by-pixel basis. The mask encodes:
      1. Pre-contrast background thresholding
      2. Minimum PE thresholding (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 in a separate series (see Table 1)
   3. Download Analysis mask files description for further information:

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.

Table 1. Series identification for derived DCE objects

1. FTV 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.
2. 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.

DICOM Dictionary for UCSF Private Attributes in Derived Objects:

Calculation parameters and DCE volume analysis results are included in private attributes in some of the derived objects. ACRIN 6698 ISPY2 Shared Private Tag Data Dictionary and ACRIN 6698 ISPY2 DWI and DCE MRI Data Descriptions files are provided for download for researchers wishing to use these parameters and/or results from the primary analyses. Note: the DCE functional tumor volume (FTV) results stored in the SER derived objects are NOT identical to those used in the I‑SPY 2 study due to differences in implementations on different platforms (UCSF in-house software vs. Hologic Inc. AEGIS system). While the differences are generally small and the AEGIS system was validated against the UCSF results in the prior I‑SPY 1 TRIAL, identical results cannot be guaranteed.

Publications by the Dataset Authors

The authors recommended this paper as the best source of additional information about this dataset:

• Li, W., Newitt, D. C., Gibbs, J., Wilmes, L. J., Jones, E. F., Arasu, V. A., Strand, F., Onishi, N., Nguyen, A. A.-T., Kornak, J., Joe, B. N., Price, E. R., Ojeda-Fournier, H., Eghtedari, M., Zamora, K. W., Woodard, S. A., Umphrey, H., Bernreuter, W., Nelson, M., … Hylton, N. M. (2020). Predicting breast cancer response to neoadjuvant treatment using multi-feature MRI: results from the I-SPY 2 TRIAL. In npj Breast Cancer (Vol. 6, Issue 1). Springer Science and Business Media LLC. https://doi.org/10.1038/s41523-020-00203-7

No publications by dataset authors were found.

Research Community Publications

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