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All objects have been deidentified to preserve patient privacy. If any evidence of non-HIPPA compliant patient PHI is found please notify the Image Analysis core lab at: UCSF Breast Imaging Research Program core lab, c.o. david.newitt@ucsf.edu .(BIRP) .

Table 1: Patient and study identification attributes included in all DICOM objects

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Signal Enhancement Ratio (SER) is a combined enhancement/washout measure derived from dynamic contrast enhanced MRI scans. Three time-points are used: pre-contrast injection, early post-contrast, and late post-contrast. Each acquisition is a high spatial resolution, 3D, T1-weighted scan. Sequential (non-centric) phase encoding is used to ensure that the effective acquisition time for time-points 2 and 3 can be taken as the time from contrast injection to the midpoint of the MRI scan. This time is generally 0.75 to 2.5 minutes after injection for the early time-point, and 7.5 minutes or greater for the late time-point. Initial validation studies and the ACRIN 6657 protocol were done with MRI acquisition duration of 5 minutes, with post-contrast scan timings of 2.5 and 7.5 minutes.
Tumor vascularity can be characterized by the percent enhancement (PE) of a post-contrast time-point S₁, from the pre-contrast time-point S₀, which reflects contrast uptake in the tissue and is given by .SER, given by the ratio of the PE at the early post-contrast time to the PE at the late post-contrast time, adds a measure of the washout rate in the tissue. SER is given by: .SER is a three-point approximation of the contrast-enhancement curve that has previously been shown to correlate well with tumor microvessel density and tumor grade, with promising prognostic value for breast cancer. Both PE and SER are calculated on a per-pixel basis.
We calculate functional tumor volume (FTV) using a semi-automated tumor segmentation algorithm based on the PE and SER maps. To avoid including skin and chest wall enhancement and imaging artifacts, analysis is limited to an operator selected rectangular volume of interest (VOI). The VOI is usually drawn on a set of orthogonal maximal intensity projection (MIP) images taken either from the early post-contrast image or from a subtraction image S₁-S₀. For a minority of cases it is also necessary for the operator to draw one or more irregularly shaped exclusion regions to eliminate non-tumor enhancement regions that can not be excluded with the rectangular VOI. All further processing is fully automatic. A map consisting of the SER of each voxel is calculated using 3 levels of filtering: a pre-contrast intensity background mask level set to 60% of the 95^th percentile intensity of the VOI is used to reduce spurious noise and to exclude low signal regions such as suppressed adipose tissue and strongly enhancing vessels; a PE threshold, typically 70%, at the early post-contrast time point is applied to segment malignant tissue from normal appearing tissue; a connectivity test is applied to the combined background and PE threshold mask, requiring a minimal number of connected neighboring voxels, to eliminate speckle noise. An SER color map is generated for qualitative assessment, showing areas of strong enhancement and washout (SER>0.9) in a gradation of colors from white to green, while enhancing but non-washing out tissue (SER<0.9) is shown in blue. FTV_PE is calculated by summing the volumes of all voxels within the VOI passing all the filtering steps and having a positive SER. Inclusion of the low SER component of the map was found to be beneficial to getting a useable FTV measure in post-chemotherapy pre-surgery examinations where enhancement values are significantly depressed relative to pre-treatment values. FTV_SER, measured similarly but with a lower limit of SER > 0.9, giving a volume measure of the washout regions of the lesions, was also investigated.
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