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MRI Studies

Trial time points for MRI studies

The primary aim of ACRIN 6698 was the evaluation of breast diffusion weighted imaging (DWI) for the prediction of response to neoadjuvant chemotherapy (NAC) for invasive breast cancer. For this purpose, serial MRI studies were acquired over the course of treatment. The study schema for the ACRIN 6698 Trial is shown in Figure 1

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Figure 1. ACRIN 6698 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 a minimum of three required acquisitions:

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For test/retest MRI studies the patient was initially positioned in the scanner and had scout, T2w and DWI acquisitions performed. The patient was then removed from the scanner bed and repositioned. The scout, T2w and DWI were repeated and then the DCE scans were conducted. All acquisitions were stored in a single MRI study for this collection.

Derived object series:

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 cases modifications may have occurred in subsequent processing.

DWI “Package” for each study with analyzable diffusion scan

1. 4 b-value DW Trace Images
   1. Multiple 2-b MSMB DWI acquisitions were combined (1 site)
   2. 3 directional DW images were geometrically averaged to generate trace images for studies where directional DWI data was saved
2. 4-b value ADC maps
   1. A low threshold (b=0 image > 10) was applied to all studies
   2. ADC calculated as linear fit to log(S(b)) = log(S(0)) – ADC * b
   3. Voxels below threshold or with ADC < 0.0 are set to 0
3. Manually defined multi-slice tumor segmentations
   1. ROIs defined for published primary analysis
   2. Tumor segmented on all slices with identifiable tumor referencing high-b image, ADC map, and DCE subtraction image (for localization)
   3. The segmentations are provided both as DICOM SEG objects and as DICOM MRI objects on TCIA

These DWI derived series can be identified either by Series Description (0008,103e) or by Series Number (0020,0011). See Table 1 for series identification details.

Manual DWI Whole-Tumor Segmentation Method

The segmentations provided in the derived diffusion objects are those generated for and used in the primary analysis and test/retest analyses for the ACRIN-6698 study. Tumor was identified on post-contrast DCE subtraction images and then localized on the ADC map. (apparent diffusion coefficient) Multi-slice, whole-tumor regions of interest (ROIs) were manually defined by selecting regions with low ADC and hyperintensity on a high b-value DWI (b=600 or 800 s/mm²) while avoiding adjacent adipose and fibroglandular tissue, biopsy clip artifacts, and regions of high T2 signal (e.g., seroma and necrosis). For multicentric/multifocal disease, all disease regions were included in the ROI. Region definition was done at the UCSF processing lab using in-house software tools developed with IDL (Exelis Visual Information Solutions, Boulder, Colorado).

DCE “Package” for each study

1. Single-breast ipsilateral (same side) 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>

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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Table 1. Series identification for derived DWI and DCE objects

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] 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.

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. A DICOM dictionary [[XXX link]] is 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.

Image Quality Control System

ACRIN 6698 analysis included use of an image quality control system developed specifically for determination of the analyzability of breast DWI for quantitative cancer treatment monitoring. The image quality control system was comprised of three sequential but independent assessment stages: protocol compliance, image quality and usability, and ROI confidence. Since protocol compliance, image quality, and ROI confidence varied between exams for the same patient, each step was performed independently for each MRI exam.

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