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Scope

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.

Patient and study identification

All patients and studies are identified through standardized, deidentified attributes as shown in Table 1.

  • Patient unique identification is provided through a 4 digit identifier set by the I-SPY TRIAL
  • Study time-point is identified through the Clinical Trial Visit Codes: T0, T1, T2, and T3
  • Imaging center discrimination has been retained (Clinical Trial Site ID) to allow for center-based analysis, but has been anonymized as codes "SITE A", "SITE B", etc…
  • In general all private DICOM attributes considered HIPPA compliant by TCIA have been retained in the image sharing submission process; but it should be noted that some studies may have been anonymized prior to submission to the analysis and archiving centers, so the presence of scanner manufacturer private attributes that may be required for some analyses can not be guaranteed.


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 (BIRP) .

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
T0 baseline
T1-n follow-ups

text

(0012,0050)

Clinical Trial Visit Description

Description for the trial visit:
baseline
early-treatment
inter-regimen
pre-surgery

text

(0012,0051)

DICOM Objects

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

 

 

 

 

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

 

 

 

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

  • Sref = reference series number: 
    S0 if S0 < 100 (GE, Siemens)
    S0/100 if S0 >= 100 (Phillips) 

** See Appendix A for SER derivation

 

 

Private attributes

Overview

The following information has been added to some or all of the DICOM objects in the data set:

  • Image quality and protocol compliance assessment
  • Timing information
  • Tumor volume of interest (VOI)
  • SER analysis parameters
  • Functional tumor volume (FTV) results

All are contained in DICOM group 0117x, labeled with a private creator field:
(0117,0010) UCSF BIRP PRIVATE CREATOR 011710xx

Image quality and protocol compliance assessment

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:
GRADE (AA=4.0 to FF=0.0)
PF (Pass/Fail or Yes/No)
SCORE (integer ratings 1,2,…)

 

CS

 

(0117,10C0)

 

> QC Factor

Quality factor evaluated

 

LO

 

(0117,10C1)

 

> QC value

Numerical quality assessment

 

DS

 

(0117,10C2)

 

> QC meaning

Meaning of quality assessment

 

CS

 

(0117,10C3)

 

> QC comment

Additional quality assessment comments

 

LT

 

(0117,10C4)

 

Protocol compliance

Protocol compliance sufficient for volume SER calculation

 

CS

 

(0117,10C5)

 

Protocol non-compliance reasons

Description of protocol compliance violation(s)

 

LO (1-n)

 

(0117,10C6)

 

 

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:
1 = Poor; 2 = Moderate; 3 = Good

SCORE

Image Quality

Quality of images aside from fat suppression
1 = Poor; 2 = Moderate; 3 = Good

SCORE

Artifact

Presence of imaging artifacts
1 = Present, 0 = Absent

PF

Overall Quality

Overall image quality for volume SER calculation
1 = Low (unusable); 2 = Intermediate; 3 = Good (usable)

SCORE

 

Timing information

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:
AUTO: Automatic based on original image meta data
MANUAL: Manually input "best-guess" timing information

LO

(0117,103A)

Timing information comments

Comments on determination of timing information

LT

(0117,103B)

 

Tumor 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 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.

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:
"VOI": Region to be analyzed
"OMIT": Region to be excluded from the analysis

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 ROI

IS

(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 analysis

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.

SER analysis parameters

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

(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) FLOAT

DS (1-n)

(0117,1018)

> Integer parameter value

Value of integer parameter
required for type (0117,1012) INTEGER

IS (1-n)

(0117,1019)

> String parameter value

Value of string parameter
required for type (0117,1012) STRING

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:

  • NONE No pre-contrast T1 masking employed
  • MANUAL Operator set pre-contrast T1 intensity threshold
  • PERCENT_MAX Pre-contrast T1 intensity threshold set to percentage of 95th percentile intensity in VOI
  • FCM Tissue mask defined by fuzzy C-means analysis

STRING

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_MAX

INTEGER

PCT_background_threshold

Background masking level percentage
Required if tissue_masking_method is PERCENT_MAX

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
target_time_2
time_tolerance
ser_correct_amp_1
ser_correct_amp_2
ser_correct_exp_1
ser_correct_exp_2

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.
For a full description see Ka-Loh Li et al, Radiology, 248 (1), July 2008, pages 79-87

FLOAT

 

Functional tumor volume (FTV) results

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)

 

I-SPY Patient Clinical Data

A set of Excel files are provided giving a subset of the clinical data collected on the study subjects. Descriptions of these data fields are provided within those files and in the attached dictionary documents:

Annotated Image Markup (AIM) Files

The FTV results will also be presented in AIM files accompanying the image data sets. [To be available at a future date.]

Appendix A: Functional Tumor Volume (FTV)1,2,3

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:
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, 2002
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, 2012
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

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