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Group | Object Group Name | Description | Format | SERIES ID * |
Images and Derived Maps |
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Original DCE MRI Volumetric Image Sets | MRI pre contrast | pre-contrast image set | DICOM Image Files | S0 (original) |
| MRI early post contrast | 2'30" (nominally) post-injection image set | DICOM Image Files | S1 (original) |
| MRI late post contrast | 7'30" (nominally) post-injection image set | DICOM Image Files | S2 (original) |
Derived DCE Image Maps | PE early | Percent signal enhancement map at the early (nominally 2'30" post-injection) time-point relative to the pre-injection baseline image: PE=100.0 * MRI(early) / MRI(pre) | DICOM Image Files | (Sref*10000) + 1001 |
| SER ** | Signal enhancement ratio (SER) map between the early (nominally 2'30" post-injection) and late (nominally 7'30" post-injection) time-points: SER=PE(early) / PE(late) | DICOM Image Files | (Sref*10000) + 1000 |
DICOM Segmentations |
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| Series ID |
Fibroglandular tissue | PE_SEG | Segmentation used for early post-contrast PE map | DICOM Segmentation objects | (Sref*10000) + 2001 |
PE thresholded SER mask | SER_SEG | Segmentation used for SER map | DICOM Image Files | (Sref*10000) + 2000 |
** See Appendix A for SER derivation
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Name | Description |
| VR (VM) * |
| DICOM Tag |
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QC Sequence | Sequence of items for each QC factor evaluated |
| SQ |
| (0117,1024) |
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> QC Type | Type of quality assessment. Defined terms: |
| CS |
| (0117,10C0) |
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> QC Factor | Quality factor evaluated |
| LO |
| (0117,10C1) |
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> QC value | Numerical quality assessment |
| DS |
| (0117,10C2) |
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> QC meaning | Meaning of quality assessment |
| CS |
| (0117,10C3) |
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> QC comment | Additional quality assessment comments |
| LT |
| (0117,10C4) |
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Protocol compliance | Protocol compliance sufficient for volume SER calculation |
| CS |
| (0117,10C5) |
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Protocol non-compliance reasons | Description of protocol compliance violation(s) |
| LO (1-n) |
| (0117,10C6) |
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Table 4: Quality assessment factors for the I-SPY 1 / ACRIN 6698 data set
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Name | Description | VR (VM) | DICOM Tag |
Total phases | Number of acquired time points (phases) including a single pre-contrast acquisition | IS | (0117,1030) |
Acquisition duration | Single phase acquisition duration | DS | (0117,1031) |
Acquisition start times | Starting time delay in seconds for each acquisition relative to the start of the 1st post-contrast acquisition | DS (1-n) | (0117,1032) |
Injection time | Assumed injection time per scanner clock | TM | (0117,1033) |
Effective acquisition delay | Effective post-injection delay for each acquisition. Non-centric phase encoding is assumed, placing the effective time half way through the acquisition | DS (1-n) | (0117,1034) |
SER timing indices | Indices (0-origin) of the 3 acquisitions used in the SER calculation | IS (3) | (0117,1035) |
Timing information method | Method used to determine the timing acquisition. Defined terms: | LO | (0117,103A) |
Timing information comments | Comments on determination of timing information | LT | (0117,103B) |
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Analysis Volume - Volume of Interest (VOI) and OMIT Regions
A 3D rectangular VOI enclosing the enhancing tumor region was defined on all cases with acceptable quality and compliance for volume SER analysis. VOI are defined in the DICOM standard patient coordinate system, as defined by the Image Position Patient (0020,0032) and Image Orientation Patient (0020,0037) fields in the original DICOM image objects. Tumor VOI attributes are described in Table 6, and are included in all derived image and segmentation objects.
In cases where significant regions of non-tumor enhancement could not be excluded from the VOI without exclusion of tumor areas , "OMIT" regions of interest (ROI) were defined to mask out these regions. OMIT ROIs were can currently be defined either as 3D rectangular VOI analogous to the analysis VOI, or as 2D irregularly shaped ROIs which were projected across the 3D image along one of the 3 orthogonal image axes. At the time of processing the I-SPY 1 / ACRIN 6657 data only the 2D irregular ROI OMIT form was available. OMIT regions are described in private attributes detailed in Table 7.
NOTE: The projected OMIT ROIs were defined on displayed orthogonal maximum intensity projection (MIP) images that had been interpolated to have isotropic voxel dimensions and were transposed where necessary to display in the standard radiologic orientations. Therefore, except for those projected along the z-axis (slice axis, projection axis (0117,1051) = 2) the stored X- and Y- vertices cannot be directly applied to the original images.
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Name | Description | VR (VM) | DICOM Tag |
VOILPS | Patient coordinate system specified rectangular VOI Sequence | SQ | (0117,1020) |
> VOILPS Center | Center of the VOI | DS (3) | (0117,1042) |
> VOILPS HalfWidth | 1st half dimension vector of the VOI | DS (3) | (0117,1043) |
> VOILPS HalfHeight | 2nd half dimension vector of the VOI | DS (3) | (0117,1044) |
> VOILPS HalfDepth | 3rd half dimension vector of the VOI | DS (3) | (0117,1045) |
> VOILPS Type | Use for the specified region. Defined terms: | CS | (0117,1046) |
VOI_pixel_start * | (x,y,z) coordinates of the first voxel in the VOI | US (3) | (0117, 10A1) |
VOI_pixel_end * | (x,y,z) coordinates of the last voxel in the VOI | US (3) | (0117, 10A2) |
- VOI_pixel_start and VOI_pixel_end are defined in cases where the Volume SER calculation was done, on the images that were used for the calculation. In out-of-protocol cases where images were acquired in the Axial plane these analyzed images will have been reformatted, cropped and/or resampled to isotropic resolution from the original images.
Table 7: DICOM Fields for description of OMIT regions: rectangular VOI and irregular projected 2D ROIs
Name | Description | VR (VM) | DICOM Tag |
OMIT regions | OMIT region sequence. Each item contains either a 3D patient-coordinate system rectangular VOI or a 2D pixel-coordinate projection ROI | SQ | (0117,1022) |
> VOILPS ROI flag | Type of VOI: enumerated values: | IS | (0117,1041) |
> VOILPS item | See Table 5 for attributes for rectangular VOI |
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> ProjectedROI npixels | Number of pixels for image used for ROI definition | US | (0117,1050) |
> Projection axis | Image pixel axis of projection for the 2D ROI. Enumerated values: 0=x-axis, 1=y-axis, 2=z-axis | IS | (0117,1051) |
> ProjectedROI transpose flag | Flag indicating ROI coordinates are defined on a transposed image | IS | (0117,1052) |
> ProjectedROI X vertices * | X-axis pixel coordinates defining the irregular ROI | US (3-n) | (0117,1053) |
> ProjectedROI Y vertices * | Y-axis pixel coordinates defining the irregular ROI | US (3-n) | (0117,1054) |
> ProjectedROI Z range * | Z-axis (plane) range of projection of the ROI. If not present the ROI was projected across all planes in the image. | US (2) | (0117,1055) |
> ProjectedROI type | Type (usage) of ROI. Defined terms: | CS | (0117,1056) |
> ProjectedROI label | Label for display with the ROI | LO | (0117,1057) |
- ROI vertices are defined on the images that were used for the volume SER calculation. In out-of-protocol cases where images were acquired in the Axial plane these analyzed images will have been reformatted, cropped and/or resampled to isotropic resolution from the original images. Furthermore, for all ROI with projection axis 0 or 1 the transpose flag and npixels values must be used to convert the stored vertices into the original image coordinate system.
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Parameters used to specify the Volume SER calculation are stored in a DICOM sequence (0117,1010) described in Table 8. Table 9 lists the parameters used, with each parameter being described in one item in the sequence. See Appendix A for a description of the Volume SER calculation.
Table 8: DICOM sequence for storing analysis parameters
Name | Description | VR (VM) | DICOM Tag |
Parameter sequence |
| SQ |
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(0117,1010) | |||
> Parameter type | Parameter type. Enumerated values: FLOAT, INTEGER, STRING | CS | (0117,1012) |
> Parameter name | Identifies parameter | LO | (0117,1014) |
> Parameter description | Description of parameter | LT | (0117,1016) |
> Floating parameter value | Value of floating point parameter | DS (1-n) | (0117,1018) |
> Integer parameter value | Value of integer parameter | IS (1-n) | (0117,1019) |
> String parameter value | Value of string parameter | LO (1-n) | (0117,101A) |
Table 9: Parameters for Volumetric Signal Enhancement Ratio (VOLSER) Analysis of Dynamic Contrast-enhanced (DCE) MRI stored in Parameter sequence (0117,1010). Each item in the sequence describes one parameter.
Name (0117,1014) | Description | Type (0117,1012) |
tissue_masking_method | Method used for pre-contrast selection of breast fibroglandular tissue regions. Defined terms: |
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pre_contrast_threshold | Intensity threshold applied to pre-contrast T1 image to select fibroglandular tissue regions. | INTEGER |
PCT_background_threshold | Background masking level percentage | INTEGER |
PE_threshold | PEthresh: early percent enhancement threshold | INTEGER |
minimum_neighbor_count | Kernel size for a minimum connectivity filter for SER analysis: voxels with fewer than this number of immediate neighbors passing the pre-contrast intensity and PE threshold tests were not included in the SER volume. | INTEGER |
ser_time_correct | Flag indicating that SER values were adjusted for scan timing. | INTEGER |
target_time_1 | Parameters used for correction of SER values for acquisitions with significant protocol timing errors. Present if and only if ser_time_correct is present and equal to 1. | FLOAT |
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Functional tumor volume (FTV = FTV(PEthresh, SERmin, SERmax) ) is defined as the volume of tissue within the tumor VOI, or otherwise segmented breast tissue region, with a PE greater than or equal to the early PE enhancement threshold (PEthresh) and an SER greater than a specified minimum SERmin and less than or equal to a specified maximum SERmax. SERmax is assumed to be infinite if not specified. Calculated FTV values are stored in the DICOM segmentation objects using the sequence described in Table 10. For the I-SPY 1 / ACRIN 6657 data set two FTV are reported: FTVPE (PEthresh, SERmin=0.0, SERmax=∞) and FTVSER (PEthresh, SERmin=0.9, SERmax=∞), where PEthresh was set empirically for each imaging center.
Table 10: DICOM sequence for storing functional tumor volume (FTV) results
Name | Description | VR (VM) | DICOM Tag |
FTV Sequence | MRI SER FTV results | SQ (1-n) | (0117,10B0) |
> SER Minimum | Minimum value of SER | DS | (0117,10B1) |
> SER Maximum | Maximum value of SER: assumed to be infinite if not specified | DS | (0117,10B2) |
> Voxel count | FTV number of voxels | IS | (0117,10B3) |
> Volume | FTV in cc | DS | (0117,10B4) |
> Label | Display label for FTV result | LO | (0117,10B5) |
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A
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set of Excel files
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are provided giving a subset of the clinical data collected on the study subjects.
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Table 11: Patient Data Dictionary
Variable Name | Variable Description | Format |
ISPY_ID | I-SPY ID de-identifies a patient's CALGB and ACRIN ID | Integer |
DataExtractDt | Date clinical data was downloaded from the CALGB database | Date format |
Patient Demographics |
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AgeCat | Patient Age Category | Number |
Age | Patient Age | Number |
Race_id | Patient Race | Number |
Sstat | Survival Status | Number |
SurvDtD | Survival date (time from study entry to death or last follow-up; time unit is days | Number |
RFS | Recurrence-free survival time – time from neoadjuvant chemotherapy start date until earliest: local or distant progression or death (time unit is days) | Number |
RFS_ind | Recurrence-free survival indicator 1=event (local or distant progression or death) | Number |
ERpos | Estrogen Receptor Status (Allred Score or Community determined), pre-treatment | Number |
PgRpos | Progesterone Receptor Status (Allred Score or Community determined), pre-treatment | Number |
HR Pos | Hormone Receptor Status, pre-treatment | Number |
pCR | Pathologic Complete Response, post-neoadjuvant (no residual invasive disease in breast or lymph nodes; presence of only in situ disease are considered disease free): | Number |
RCBClass | Residual Cancer Burden class: | Number |
RCB Index | Residual Cancer Burden Index: | Number |
Descriptions of these data fields are provided within those files and in the attached dictionary documents:
Patient Clinical Data | DataDict - TCIA Shared Patient Clinical |
Patient Outcome Data | DataDict - TCIA Shared Outcome |
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The FTV results will also be presented in AIM files accompanying the image data sets. [To be available at a future date.]
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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 95th 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. FTVPE 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. FTVSER, 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.
For further information see:
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3.ACRIN PROTOCOL 6657 / CALGB 150007 http://www.acrin.org/6657_protocol.aspxContrast-Enhanced Breast MRI for Evaluation of Patients Undergoing Neoadjuvant Treatment for Locally Advanced Breast Cancer