RADIOLOGY
RESEARCH
Current DICOM Topics:
1. The new surface segmentation class
2. Compression: JPEG 2000 & MPEG2
Donald Peck, PhD
Michael Flynn, PhD
Recent DICOM Enhancements
that are important to Medical Physicists
AAPM 2008
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CT Radiation Dose Reporting
X-Ray 3D Storage SOP Class
Email Transport
Enhanced PET Image
Deformable Spatial Registration Storage SOP Class
Breast Tomosynthesis Image Storage SOP Class (Ballot)
Segmentation Storage SOP Class
Surface Segmentation Storage SOP Class (Ballot)
JPEG 2000 Interactive Protocol
JPEG 2000 Part 2 Multi-component Transfer Syntaxes
2
Part I
• Surface Segmentation Storage SOP Class
Part II
AAPM 2008
• Compression: JPEG 2000 and MPEG2
3
DICOM Review
• Utilizes an open standards development
process that encourages the involvement
and consensus of both vendors and users
AAPM 2008
• Specification of a conformance mechanism
so that a user can decide whether or not
devices are likely to interoperate
4
DICOM Review
• DICOM Standards Committee (DSC)
• DICOM’s executive body whose members
are imaging equipment manufacturers,
physician organizations, and others
• 26 manufacturer members
• 20 other members
• DICOM's activities are coordinated
through a general secretariat at MITA
AAPM 2008
• formerly NEMA
5
DICOM Standards Committee (DSC)
• Development of DICOM Standard is done
through committees termed “Working
Groups” (WG)
• AAPM Members can participate in any WG
to develop the Standard
AAPM 2008
• WG propose work items based on
suggestions from members or at the
direction of the DSC
6
DICOM “workflow”
• Work items are divided into Supplements
and Change Orders
• Supplements define new objects, content or
structure
AAPM 2008
• Change Orders modify the existing
Standard
7
DICOM “workflow”
• Output of any work item is submitted to
the Base Standards Working Group (WG6)
for review throughout the process
• WG6 may request changes or clarification to
the work item to ensure it complies with
Standard
AAPM 2008
• Once the work item is complete WG6
petitions the DSC to approve work item and
send out for public comment
8
DICOM “workflow”
• After public comment and all issues listed in the
comments are responded to, the DSC authorizes
the work item for letter ballot by DICOM
members
• Change proposals do not require the same rigorous
review process and are often “batched” for public
comment and letter ballot,
AAPM 2008
• Some Change proposals can be instituted without
comment or ballot if the change is required to
reduce potential patient care issues or it is
typographical or trivial in nature
9
Changes to Standard
• Currently over 100 approved Supplements
incorporated into Standard
• Over 25 in progress or in comment stage
• Currently over 600 Change Proposals
incorporated into Standard
AAPM 2008
• Ongoing process with changes being
reviewed at every WG6 meeting
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AAPM 2008
DICOM Parts
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PS
PS
PS
PS
PS
PS
PS
PS
PS
PS
PS
PS
PS
PS
PS
PS
3.1
3.2
3.3
3.4
3.5
3.6
3.7
3.8
3.10
3.11
3.12
3.14
3.15
3.16
3.17
3.18
Describes how the
Standard is organized
Introduction and Overview
Conformance
Information Object Definitions
Service Class Specifications
Data Structures and Encoding
Data Dictionary
Message Exchange
Network Communication Support for Message Exchange
Media Storage and File Format for Data Interchange
Media Storage Application Profiles
Media Formats and Physical Media for Data Interchange
Grayscale Standard Display Function
Security Profiles
Content Mapping Resource
Explanatory Information
Web Access to DICOM Persistent Objects (WADO)
11
Changes to the Standard
AAPM 2008
On a yearly basis all changes to the Standard are
published at: http://medical.nema.org/dicom/
12
Surface Segmentation Storage SOP Class
• Supplement 132, currently under revision
following Letter Ballot
AAPM 2008
• Developed by a joint effort of WG 17 (3D)
and WG 24 (Surgery)
13
Current DICOM Objects
• All images are stored as 2D frames
• If more than one image is acquired, and there is
some information linking the images (e.g. cross
sectional images, temporal images, etc.) the images
can be stored as multi-frame objects
AAPM 2008
• The images are still single 2D frames
14
Current DICOM Objects
• 3D reconstructions can be created from the multiframe objects
AAPM 2008
• Yet results can only be saved as “snapshots” of
specific views (i.e. single- or multi-frame images)
15
Rendering of 3D objects
• Surface renderings
are commonly
derived from
polygonal surface
primitives
AAPM 2008
• Need a method in
DICOM to store
these primitives
instead of images
From Osirix
16
Surface Segmentation Storage SOP Class
• All surfaces used for 3D objects first
require the objects to be segmented
• Supplement introduces a new Surface Mesh
Module that may be used to encode the
segmentation data
AAPM 2008
• The Surface Segmentation can specify a
surface derived from any DICOM modality
or from non-DICOM measurement
techniques.
• Can be used to specify designed surfaces,
e.g. implants.
17
The supplement supports the following features:
• The segmentation shapes are encoded in a
polygonal representation of the surface.
• More than one segmentation object is supported
per Imaged Object Definition (IOD) instance.
• Position and orientation are defined within the
patient coordinate system as specified by the
Frame of Reference.
AAPM 2008
• Segmentation is in the patient space rather than the
image data, i.e. it is not slice based.
18
Surface Mesh Primitives
• Encoded information was developed to allow
easy utilization of the object data by
graphic hardware and software
AAPM 2008
• The encoded data has the format of simple
“primitive” structures.
19
Surface Mesh Primitives
• Vertex - a single vertex, referencing a single point
• Edge - an edge, referencing two points
AAPM 2008
• Line - a series of connected points describing a path
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Surface Mesh Primitives
• Triangle - a triangle, referencing three points
AAPM 2008
• Triangle Strip - a triangle strip with n triangles
21
Surface Mesh Primitives
• Triangle Fan- a set of triangles where one point is
within each triangle, i.e. the center of the fan.
AAPM 2008
• Facet - a planar polygon, referencing n points
A Facet can be easily made
from Triangles, but inclusion
of this primitive allows less
points to be saved
22
AAPM 2008
Information Encoded
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Segmentation algorithm used to create the surface
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Whether post processing has been done on the
segmented surface
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Recommended display/presentation properties
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If the surface is a finite volume or is a manifold
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Normal to surface
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Segmentation Algorithms
AAPM 2008
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
Neighborhood Analysis
Adaptive Filtering
Edge Detection
Morphological Operations
Histogram Analysis
Multi-Scale/Resolution Filtering
Cluster Analysis
Multispectral Processing
Manual Processing
Artificial Intelligence
Deformable Models
This is a required attribute, i.e. Type 1
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Surface processing
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Surface modification such as smoothing
operations, which remove redundant
vertices, or decimation which will modify
the resolution of the surface.
AAPM 2008
•
Can reduce the amount of data needed to
define the surface
Algorithm description and data reduction ratio
are required if this processing is done,
i.e. this attribute is a Type 2
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Recommended Presentation
• Recommended Presentation Opacity
• Percentage of transmission of light through the
surface.
• Recommended Presentation Type
• Defined terms are:
• SURFACE; Render the surface as a solid, applying the
opacity specified.
• WIREFRAME; Represent the surface as a series of
lines connecting the vertices to form the defined
primitive faces.
AAPM 2008
• POINTS; Represent the surface as a cloud of points.
These are all required attributes
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Finite Volume
• A Finite Volume is defined when the
surface mesh generated by the primitives
is topologically closed and has an inside
and an outside.
• A surface mesh is closed if it has no rim
(every facet has a neighboring facet along
each edge).
• Not all closed surfaces contain a finite
volume or are required to considered a
finite volume
AAPM 2008
This is a required attribute
These points can be defined to contain
one or two closed/finite volumes
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Manifold objects
This is a required attribute
• A surface embedded into an n-dimensional vector
space is called an n-1 manifold if it resembles an
n-1 dimensional Euclidian space in a neighborhood
of every point lying on the surface.
• A sphere in 3D-space is a 2-dimensional manifold:
AAPM 2008
Every point has a neighborhood that looks like a plane.
Shared points along central surface
makes these two tetrahedrons
Non-Manifold
Object is a Manifold
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Surface normal determinations
• If the “normal” for every surface
point is provided, the normal for a
primitive may be computed by
combining the normal's for each
vertex making up the primitive.
AAPM 2008
• If the Normal for all surface points
are not provided, the normal for a
primitive shall be determined by
computing the cross product of the
primitive segments.
• The primitive vertices are taken in
the order specified within the
Primitive Point Index List attribute.
29
Current Issues
• Back from Letter Ballot
• Formatting of the Supplements grammatical
structure was a concern, so edits are in
progress
AAPM 2008
• Should be approved October 2008
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Part I
• Surface Segmentation Storage SOP Class
Part II
• Compression: JPEG 2000 and MPEG2
AAPM 2008
• Previous JPEG 2000 compression standards
are now extended to support progressive
web communication using JPIP.
• Previous MPEG2 standards are being
extended to support high resolution objects.
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Topics
AAPM 2008
A.
B.
C.
D.
E.
F.
Basic Concepts
JPEG 2000
JPEG 2000 p2 – JPIP
JPEG 2000 p2 – 3D
MPEG2 MPML & MPHL
Image Quality
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Encode - Decode
• Encode
Transform the digital image pixel data into
a binary code stream of reduced size.
• Decode
AAPM 2008
Interpret a compressed code stream to
retrieve the original image pixel data.
33
Image management
AAPM 2008
A basic image management system will store and
transmit image data in the acquired image format
ACQUISITION
STORAGE
TRANSMISSION
PRESENTATION
8 MB
8 MB
8 MB
8 MB
34
Image management
AAPM 2008
Reversible (lossless, bit-preserving) compression
• Storage and transmission size reduced by a factor of 2-3
• Decoded images values are identical to the original
ACQUISITION
STORAGE
TRANSMISSION
PRESENTATION
8 MB
3 MB
3 MB
8 MB
35
Image management
AAPM 2008
Irreversible (lossy) compression
reduces bit storage and transmission by a factor of 10 or
more, however the decoded image values are slightly altered.
ACQUISITION
STORAGE
TRANSMISSION
PRESENTATION
8 MB
0.5 MB
0.5 MB
8 MB
36
Compression ratio
• Compression ratio,
The size of the original image data is related to
the size of the encoded data
AAPM 2008
2:1 , 8:1 , 16:1 , 80:1
• Bit-rate,
The average bits per pixel computed from the
size of the encoded data.
8 , 2 , 1.0 , 0.2
The bit-rate is generally a better indicator of
image distortion for irreversible compression.
37
Topics
AAPM 2008
A.
B.
C.
D.
E.
F.
Basic Concepts
JPEG 2000
JPEG 2000 p2 – JPIP
JPEG 2000 p2 – 3D
MPEG2 MPML & MPHL
Image Quality
38
DICOM SUP 61 (2002), JPEG 2000
• Retired 14 unused JPEG transfer syntaxes
• Retained;
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•
1.2.840.10008.1.2.4.50
1.2.840.10008.1.2.4.51
1.2.840.10008.1.2.4.70
1.2.840.10008.1.2.4.80
1.2.840.10008.1.2.4.81
1.2.840.10008.1.2.5
AAPM 2008
• Added;
• 1.2.840.10008.1.2.4.90
• 1.2.840.10008.1.2.4.91
JPEG baseline 8 bit
JPEG baseline 12 bit
JPEG lossless
JPEG LS lossless
JPEG LS lossy
RLE lossless
JPEG 2000 lossless
JPEG 2000
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DICOM part 3.5 – Data Structures and Encoding
From DICOM part 3.5 we learn,
• Pixel data conveyed in the Pixel Data Element
(7FE0,0010) may be sent either in a Native
(uncompressed) Format or in an Encapsulated
Format (e.g. compressed) defined outside the
DICOM standard.
AAPM 2008
• If sent in an Encapsulated Format (i.e. other than
the Native Format) the Value Representation OB is
used. The Pixel Cells are encoded according to the
encoding process defined by one of the negotiated
Transfer Syntaxes (see Annex A).
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DICOM part 3.5 – Data Structures and Encoding
DICOM part 3.5 further explains,
• Inclusion of a JPEG 2000 coded image in a DICOM
message is indicated by the use of specific
Transfer Syntaxes that are defined in Annex A.
• Only the features defined in JPEG 2000 Part 1
(ISO/IEC 15444-1) are permitted for [the two
JPEG 2000] Transfer Syntaxes.
AAPM 2008
• Wavelet based multiple component transformations
using the same two wavelet filters as used in Part 1
of JPEG 2000 (5-3 reversible wavelet and 9-7
irreversible wavelet).
• A single JPEG 2000 process is used for bit depths
up to 16 bits.
41
DICOM part 3.5 – Data Structures and Encoding
DICOM part 3.5 further explains,
• Note in particular that the JP2 file header is
not sent in the JPEG 2000 bitstream that is
encapsulated in DICOM.
*.jpg – image compressed using the jpeg standard.
AAPM 2008
*.jp2 – image compressed using jpeg 2000.
‘Similar to JPEG-1, JPEG2000 defines both a
file format and a code stream. Whereas the
latter entirely describes the image samples, the
former includes additional meta-information as
the resolution of the image ... ‘
en.wikipedia.org/wiki/JPEG2000
42
J.P.E.G.
• The Joint Photographic Experts Group (JPEG) is a joint
committee between ISO and ITU-T which created the
JPEG and JPEG 2000 standards.
• Its proper name is ISO/IEC Joint Technical Committee 1,
Subcommittee 29, Working Group 1.
• Resources;
• www.jpeg.org
• the jpeg committee home page
• www.ece.uvic.ca/~mdadams/jasper/
• the Jasper project,
• open source JPEG 2000 reference implementation.
AAPM 2008
• www.kakadusoftware.com
• highly conformant, very fast,
• nearly free software for JPEG 2000 and JPIP .
43
DICOM SUP 61 (2002), JPEG 2000
The introduction of Supplement 61 notes;
• The use of [JPEG 2000] does not necessarily result in
improved compression performance for any particular
application in terms of
• quantitative or qualitative measures of image fidelity,
• preservation of diagnostically significant information,
• consumption of resources (memory, [encode/decode] speed).
AAPM 2008
• However, JPEG 2000 offers additional features that may
be important for some medical applications. These
features include;
• progressive and embedded spatial and contrast resolution,
• progression to lossless reconstruction,
• regions of interest and ...
44
JPEG 2000 - features
Multiple resolution representation
AAPM 2008
• JPEG2000
decomposes the image
into a multiple
resolution
representation in the
course of its
compression process.
• This representation
can be put to use for
other image
presentation purposes
beyond compression
as such.
45
JPEG 2000 - features
Progressive transmission by pixel and resolution accuracy
•JPEG2000 provides efficient
code-stream organizations which
are progressive by pixel accuracy
and by image resolution.
AAPM 2008
•After a small part of the whole
file has been received, the viewer
can see a low quality version of
the final picture.
•The quality then improves
progressively by downloading
more data bits from the source.
46
Image management
AAPM 2008
Progressive transmission
• Some clients can view the original image
• Other clients can view with slightly altered image values
ACQUISITION
STORAGE
TRANSMISSION
PRESENTATION
8 MB
3 MB
3 MB
8 MB
47
Topics
AAPM 2008
A.
B.
C.
D.
E.
F.
Basic Concepts
JPEG 2000
JPEG 2000 p2 – JPIP
JPEG 2000 p2 – 3D
MPEG2 MPML & MPHL
Image Quality
48
DICOM SUP 106 (2006), JPIP
DICOM JPIP REFERENCED TRANSFER SYNTAX
1.2.840.10008.1.2.4. 94
“This Supplement extends the Pixel Data Module to
allow reference to a JPIP URL to access pixel data,
rather than encoding it in the image instance.”
AAPM 2008
“Data Element (7FE0,0010) Pixel Data shall not be
present, but rather pixel data shall be referenced via
Data Element (0028,7FE0) Pixel Data Provider URL”
49
AAPM 2008
DICOM with JPIP: Diagram
Weisfeiler, Dicom WG4, Feb 2006
50
AAPM 2008
JPIP Application Block Diagram
Weisfeiler, Dicom WG4, Feb 2006
51
Image Streaming GUIs
AAPM 2008
JPIP facilitates advanced image viewing GUIs
52
DICOM PS 3.18 - 2008
Web Access to DICOM Persistent Objects (WADO)
Annex B - Examples (Informative)
B.3 RETRIEVING A REGION OF A DICOM IMAGE
AAPM 2008
Retrieving a region of a DICOM image, converted if possible in JPEG2000,
with annotations burned into the image containing the patient name and technical
information, and mapped into a defined image size:
https://aspradio/imageaccess.js?requestType=WADO
&studyUID=1.2.250.1.59.40211.12345678.678910
&seriesUID=1.2.250.1.59.40211.789001276.14556172.67789
&objectUID=1.2.250.1.59.40211.2678810.87991027.899772.2
&contentType=image%2Fjp2;level=1,image%2Fjpeg;q=0.5
&annotation=patient,technique
&columns=400
&rows=300
&region=0.3,0.4,0.5,0.5
&windowCenter=-1000
&windowWidth=2500
53
Topics
AAPM 2008
A.
B.
C.
D.
E.
F.
Basic Concepts
JPEG 2000
JPEG 2000 p2 – JPIP
JPEG 2000 p2 – 3D
MPEG2 MPML & MPHL
Image Quality
54
DICOM SUP 105 (2005), JPEG 2000 p2 - Multi-component
This supplements adds support for the
multi-component extensions in part 2 of
the JPEG 2000 standard.
• 1.2.840.10008.1.2.4.92
JPEG 2000 Part 2 Multicomponent
Image Compression (Lossless Only)
AAPM 2008
• 1.2.840.10008.1.2.4.93
JPEG 2000 Part 2 Multicomponent
Image Compression
55
DICOM SUP 105 (2005), JPEG 2000 p2 - Multi-component
Multicomponent transforms for 3D compression
AAPM 2008
• The multi-component transformations in Part 2 of JPEG
2000 can be effective in compressing volumetric
datasets because the correlation between adjacent
images can be exploited to achieve better compression
than if each image were compressed independently.
• The use of component collections is advantageous for
3D imagery that is highly correlated over a small
number of components (slices), but less correlated over
the entire sequence. Image data can then be retrieved
from within the 3D stack (unlike video codecs)
56
3D Compression performance
512 x 512 CT, 620 slices
AAPM 2008
15:1
40:1
Tzannes, RSNA, 2003
57
Topics
AAPM 2008
A.
B.
C.
D.
E.
F.
Basic Concepts
JPEG 2000
JPEG 2000 p2 – JPIP
JPEG 2000 p2 – 3D
MPEG2 MPML & MPHL
Image Quality
58
DICOM SUP 42 (2004), MPEG2 MP@ML
Supplement 42
• Working Group 13, Visible Light, 2004
• A DICOM Transfer Syntax for MPEG2
Image Compression shall be identified
by a UID value of
1.2.840.10008.1.2.4.100
AAPM 2008
corresponding to MPEG2 MP@ML option
of the ISO/IEC MPEG2 Video standard.
• Annex X, DVD MPEG2 Interchange
Profiles (includes DICOMDIR).
59
MPEG2
• MPEG2 is a widely used format for
broadcast and cable television and for DVD
video programs.
• MPEG2 Profiles and Levels
AAPM 2008
• The Main profile (MP) applies to square pixels
in 4:3 or 16:9 format (not scalable).
• Main Level (MP) – 720 x 576 (15 Mb/S) max
• High Level (HL) – 1920 x 1152 (80 Mb/S) max
60
DICOM SUP 137 (2008 public comment), MPEG2 MP@HL
• This Supplement describes a new
transfer syntax to embed an additional
higher level of MPEG2 encoding in
DICOM.
AAPM 2008
• The syntax uses MPEG2 lossy
compression permitting higher spatial
resolution quality, called Main Profile /
High Level (MP@HL), that does not
exceed 80 Mbit/s. This goes beyond the
data rates typically defined by the "Bluray” consortium.
61
DICOM SUP 137 (2008 public comment), MPEG2 MP@HL
• The syntax would typically be used for
encoding HD video sequences, though it
is not constrained from encoding other
forms of multi-frame pixel data.
AAPM 2008
• Targeted modalities include microscopic
and endoscopic applications such as
Gastro-Enterology, Laparoscopy,
Orthopedics, Ophthalmology, ENT,
Gynaecology, Bronchoscopy, Pathology,
and (Microscopic) Surgery.
62
MPEG2 vs MPEG4
MPEG4 is widely used in computer video
applications. It was not used in this
supplement because;
AAPM 2008
• MPEG2 is supported by well-established
equipment and applications. In particular,
tools for editing MPEG2 video are more
available in the short term than for MPEG4.
• By comparison with MPEG2, software
decoding of MPEG4 is more computationally
intensive and may be possible in the short
term only with high end computer terminals
or with hardware assistance.
63
Topics
AAPM 2008
A.
B.
C.
D.
E.
F.
Basic Concepts
JPEG 2000
JPEG 2000 p2 – JPIP
JPEG 2000 p2 – 3D
MPEG2 MPML & MPHL
Image Quality
64
Foos, SPIE, 2000
Compressed Radiographic Image Quality
Average Ratings
7 obs , 5 imgs
No Difference
9
8
Just Noticeable
7
6
Conspicuous
Statistical Groupings
5
f97
f97_csf
CR Portable Chest
CR Shoulder
Thoravision
Digitized Film
Flat Panel Digital
4
Significant
3
AAPM 2008
2
Unacceptable
1
0.00
0.50
1.00
1.50
Bits-Per-Pixel
f97_csf_msk
wtcq_lra_csf
I53_csf
jpeg_csf
2.00
2.50
65
Side
To
Side
Canon 50g, 160 micron pixel
AAPM 2008
IQ
1 b/pix
16:1
66
Replace
Canon 50g, 160 micron pixel
AAPM 2008
IQ
1 b/pix
16:1
67
Flicker
Canon 50g, 160 micron pixel
AAPM 2008
IQ
1 b/pix
16:1
68
Subtract
Canon 50g, 160 micron pixel
AAPM 2008
IQ
1 b/pix
16:1
69
Canadian Compression Standard
Canadian Association of Radiologists
Standards for Irreversible
Compression in Digital Diagnostic
Imaging within Radiology
Approved June 2008
• Two independent literature reviews, sponsored by Canada Health
Infoway, were completed as a part of the study
• Two independent and comprehensive legal reviews, sponsored by
Canada Health Infoway, were completed as a part of the
broader study into the use of irreversible compression.
AAPM 2008
• Reference ACR and FDA positions on irreversible compression.
• CAR sponsored a pan Canadian clinical evaluation on JPEG-2000
irreversible compression in medical imaging. The evaluation
project was directed by Dr. David Koff, Sunnybrook Hospital .
www.car.ca
70
Questions?
AAPM 2008
?
71
Comment
• AAPM has recently applied to
become a member organization of
the DICOM Standards Committee.
AAPM 2008
• Members are being solicited for
participation in specific working
groups that are closely aligned with
Medical Physics.
72