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This document contains definitions for the DICOM objects and attributes specific to the ACRIN 6657/I-SPY 1 MRI image data collection, and descriptions of associated data provide with this image data set.
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All patients and studies are identified through standardized, deidentified attributes as shown in Table 1.
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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 UCSF Breast Imaging Research Program core lab, c.o. david.newitt@ucsf.edu .
Table 1: Patient and study identification attributes included in all DICOM objects
Variable Name | Variable Description | Format | DICOM Tag |
Patient Name | Encoded patient ID (pppp), ACRIN Protocol ID, study name | pppp^6657^ISPY1 | (0010,0010) |
Patient ID | Study name and patient ID | ISPY1_pppp | (0010,0020) |
Clinical Trial Patient ID | Unique identification for patient in the trial | Number:pppp | (0012,0040) |
Clinical Trial Site ID | Code of the trial site:"SITE x" | text | (0012,0030) |
Clinical Trial Visit Code | ID code for the trial visit | text | (0012,0050) |
Clinical Trial Visit Description | Description for the trial visit: | text | (0012,0051) |
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Table 2 details the DICOM objects provided by the UCSF core lab in the I-SPY 1 / ACRIN 6698 shared data set on TCIA. Not all objects will be present in all cases due to unanalyzable studies. Original image objects are unprocessed except for necessary conversion to DICOM and deidentification. Derived image objects, including standardized early time-point percent enhancement (PE) and signal enhancement ratio (SER) maps, are provided for all volume-SER analyzable studies. DICOM segmentation objects representing PE analyzable breast tissue and SER volume are also provided. Parameters used in calculating the derived objects are stored in DICOM private group attribute set (0117,10xx) in each object as described below.
Table 2: DICOM Objects in shared data set
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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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 | ||||||||||
| =
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** See Appendix A for SER derivation
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The following information has been added to some or all of the DICOM objects in the data set:
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All are contained in DICOM group 0117x, labeled with a private creator field:
(0117,0010) UCSF BIRP PRIVATE CREATOR 011710xx
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Image quality and protocol compliance were assessed by the UCSF core lab for all submitted image studies. DCE images were assessed for fat suppression, image quality, and artifacts; and then given an overall quality score. In addition, studies were evaluated for protocol violations that would prohibit volume SER analysis. QC ratings are stored in a DICOM sequence, attribute tag (0117,1024), with each separate QA rating contained in an item in this sequence, as described in Table 3. In addition, overall protocol compliance is stored in separate fields as listed in Table 3. Table 4 gives details for the different QA factors.
Table 3: DICOM fields for quality assessment
Name | Description |
| VR (VM) * |
| DICOM Tag |
|
QC Sequence | Sequence of items for each QC factor evaluated |
| SQ |
| (0117,1024) |
|
> 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
Factor (0117,10C1) | Description | Type (0117,10C0) |
Fat sat | Quality of fat suppression. Integer scores: | SCORE |
Image Quality | Quality of images aside from fat suppression | SCORE |
Artifact | Presence of imaging artifacts | PF |
Overall Quality | Overall image quality for volume SER calculation | SCORE |
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WARNING: Timing information was determined to the best of the core lab's ability based on the meta information in the original images submitted. Accuracy of the timing information cannot be guaranteed. In particular, all post-contrast times are based on the assumption that the injection and the start of the 1st post-contrast scan were simultaneous, which could not be confirmed.
Timing information fields are shown in Table 5. Timing information was added to all derived image and segmentation objects.
Table 5: Scan timing information fields for dynamic contrast-enhanced (DCE) MRI
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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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 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. 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.
Table 6: DICOM Fields for rectangular VOI
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:
0rectangular VOI
1irregular projected pixel-coordinate ROIIS
(0117,1041)
> VOILPS item
See Table 5 for attributes for rectangular VOI
> 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:
OMITregion to be excluded from the analysisCS
(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.
SER analysis parametersParameters 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.Anchor _Toc285033401 _Toc285033401 Table 8: DICOM sequence for storing analysis parameters
Name
Description
VR (VM)
DICOM Tag
Parameter sequence
SQ (1-n)
(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
required for type (0117,1012) FLOATDS (1-n)
(0117,1018)
> Integer parameter value
Value of integer parameter
required for type (0117,1012) INTEGERIS (1-n)
(0117,1019)
> String parameter value
Value of string parameter
required for type (0117,1012) STRINGLO (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:
NONENo pre-contrast T1 masking employed
MANUALOperator set pre-contrast T1 intensity threshold
PERCENT_MAXPre-contrast T1 intensity threshold set to percentage of 95th percentile intensity in VOI
FCM Tissue mask defined by fuzzy C-means analysisSTRING
pre_contrast_threshold
Intensity threshold applied to pre-contrast T1 image to select fibroglandular tissue regions.
Required if tissue_masking_method is MANUAL or PERCENT_MAXINTEGER
PCT_background_threshold
Background masking level percentage
Required if tissue_masking_method is PERCENT_MAXINTEGER
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
target_time_2
time_tolerance
ser_correct_amp_1
ser_correct_amp_2
ser_correct_exp_1
ser_correct_exp_2Parameters 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.
For a full description see Ka-Loh Li et al, Radiology, 248 (1), July 2008, pages 79-87FLOAT
Functional tumor volume (FTV) resultsFunctional 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.Anchor _Toc285033402 _Toc285033402 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)
I-SPY Patient Clinical DataA separate set of files will be available giving a subset of the clinical data collected on the study subjects. Table 11 describes the data provided. More extensive patient data is available through I-SPY [ref].Anchor _Toc285033403 _Toc285033403 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
1001-1239DataExtractDt
Date clinical data was downloaded from the CALGB database
Date format
mm/dd/yyyyPatient Demographics
AgeCat
Patient Age Category
1= 18-30
2= >30-40
3= >40-50
4= >50-60
5= >60-70
6= >70-80
7= >80-<89Number
Age
Patient Age
Number
Race_id
Patient Race
1=Caucasian
3=African American
4=Asian
5=Native Hawaiian/Pacific Islander
6=American Indian/Alaskan Native
50=Multiple raceNumber
Sstat
Survival Status
7=Alive
8= Dead
9=LostNumber
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)
0=censor at last follow-upNumber
ERpos
Estrogen Receptor Status (Allred Score or Community determined), pre-treatment
0=Negative
1=Positive
2=IndeterminateNumber
PgRpos
Progesterone Receptor Status (Allred Score or Community determined), pre-treatment
0=Negative
1=Positive
2=IndeterminateNumber
HR Pos
Hormone Receptor Status, pre-treatment
0=Negative for both ER and PR
1=Positive if either ER or PR was Positive
2=Indeterminate if both ER and PR were IndeterminateNumber
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):
0= No (did not achieve pCR)
1= Yes
Blank= no surgeryNumber
RCBClass
Residual Cancer Burden class:
0= 0, RCB index 0
1= I, RCB index less than or equal to 1.36
2= II, RCB index greater than 1.36 or equal to 3.28
3= III, RCB index greater than 3.28
Blank= unavailable or no surgeryNumber
RCB Index
Residual Cancer Burden Index:
-Numerical value
Blank= unavailable or no surgeryNumber
Annotated Image Markup (AIM) FilesThe FTV results will also be presented in AIM files accompanying the image data sets. [To be available at a future date.]Anchor _Toc285033404 _Toc285033404
Appendix A: Functional Tumor Volume (FTV) 1,2,3Signal 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.Anchor _Toc285033405 _Toc285033405
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:
1.Partridge SC, Gibbs JE, Lu Y, et al: Accuracy of MR imaging for revealing residual breast cancer in patients who have undergone neoadjuvant chemotherapy. AJR Am J Roentgenol 179:1193-9, 2002Anchor _ENREF_5 _ENREF_5
2.Hylton NM, Blume JD, Bernreuter WK, et al: Locally advanced breast cancer: MR imaging for prediction of response to neoadjuvant chemotherapy--results from ACRIN 6657/I-SPY TRIAL. Radiology 263:663-72, 2012Anchor _ENREF_9 _ENREF_9
3.ACRIN PROTOCOL 6657 / CALGB 150007 http://www.acrin.org/6657_protocol.aspx Contrast-Enhanced Breast MRI for Evaluation of Patients Undergoing Neoadjuvant Treatment for Locally Advanced Breast Cancer