DICOM and Slicer: A Tutorial

DICOM and Slicer:
A Tutorial
Sonia Pujol, Ph.D.
Assistant Professor of Radiology
Director of 3D Slicer Training & EducaDon
Brigham and Women’s Hospital
Harvard Medical School
spujol@bwh.harvard.edu
1
ObjecDve
This tutorial provides a basic introducDon to

the DICOM standard, and shows how to
visualize DICOM images in 3D Slicer version 5.0
Sonia Pujol PhD, All Rights Reserved 2

Tutorial Outline
Part 1: IntroducDon to DICOM
Part 2: DICOM and Slicer
Part 3: Loading and Visualizing DICOM data in Slicer

Tutorial material
3D Slicer version 5.0
hVps://download.slicer.org

SlicerDICOMTutorialData
DICOM Torso CT
DICOM Breast MRI

•  3D Slicer is a free open source soXware
applicaDon distributed under a BSD style
license
Disclaimer
•  The soXware is not FDA approved or CE
marked, and is for research use only
5
Sonia Pujol PhD, All Rights Reserved
Part 1: IntroducDon to DICOM

Reproducible Science
•  Reproducible science is criDcal to drive research and accelerate
discoveries
•  Open-source soXware tools such as 3D Slicer and data

standards such as DICOM contribute to the reproducibility of
scienDfic results in biomedical research

F.A.I.R. Principles
•  Findable: Data are easily findable
•  Accessible: Users know how to access the data,
including authenDcaDon and authorizaDon
•  Interoperable: Data can be integrated with
other data and can interoperate with
applicaDons for storage and analysis
•  Reusable: Data can be replicated or combined
The FAIR Guiding Principles for scien7fic for new research
data management and stewardship.
Wilkinson et al. Sci. Data 2016
hFp://go-fair.org/fair-principles

The DICOM standard
•  DICOM (Digital Imaging and CommunicaDons in Medicine) is the
internaDonal standard for handling, storing, prinDng and
transmi`ng medical imaging data
•  Clinical imaging equipment (CT scanners, MR scanners, X-Ray

and ultrasound machines) generate DICOM files

10
•  1982: The American College of Radiology (ACR) and
the NaDonal Electrical Manufacturers AssociaDon
(NEMA) iniDate standards for the interconnecDon of
medical imaging devices
•  1985: PublicaDon of the ACR-NEMA Digital Imaging

and CommunicaDons Standards version 1.0
DICOM
•  1988: PublicaDon of the ACR-NEMA Digital Imaging
History and CommunicaDons Standards version 2.0
•  1993: PublicaDon of the ACR-NEMA Standards

version 3.0 also referred to as the Digital Imaging
and CommunicaDons in Medicine (DICOM) standard

11
•  The DICOM standard is conDnuously being
refined to address new community needs
through mulDple releases every year
•  As of 2020/07/06, the DICOM standard is DICOM

PS3 2020c and contains 4,000 pages
DICOM
•  DICOM Working Groups are established to
Today expand the capabiliDes of the standard given the
conDnuous evoluDon of imaging modaliDes
(e.g. WG-16 MagneDc Resonance)
hVps://www.dicomstandard.org/wgs

FAIR Data and the DICOM Standard
The DICOM Standard facilitates compliance of imaging data

with FAIR principles

DICOM Data Model
PaDent •  In the DICOM data model, a
DICOM Study consists of several
Study DICOM Series, and each DICOM
Series contains DICOM Instances
Series Series Series

•  Each of the DICOM Studies, Series
and Instances are assigned a
Unique IdenDfier (UID)
Instances Instances Instances

Example of DICOM instances:
DICOM MRI Image data
Image001.dcm
Header
Image002.dcm
Raw Data Image003.dcm
….
An MRI image is an example of DICOM instance that consists of a DICOM

header and an image dataset
0002,0000,File Meta Elements Group Len=148
0002,0001,File Meta Info Version=256
0002,0002,Media Storage SOP Class UID=1.2.840.10008.5.1.4.1.1.4.
§  The DICOM header contains metadata
0002,0003,Media Storage SOP Inst UID=0.0.0.0.
0002,0010,Transfer Syntax UID=1.2.840.10008.1.2.1.
which include informaDon on the
…
0008,0060,Modality=MR
paDent, study and imaging data.
0008,0070,Manufacturer=GE MEDICAL SYSTEMS
0008,0080,Institution Name=1852796513
§  DICOM provides a standardized way

0008,0081,City Name=1852796513
0008,0090,Referring Physician's Name=1852796513
0008,0092,?=1852796513
0008,0201,?=-0500
0008,1010,Station Name=1852796513
to present metadata which makes it
0008,1030,Study Description=anon
0008,103E,Series Description=anon
searchable
0008,1040,Institutional Dept. Name=1852796513
0008,1050,Performing Physician's Name=1852796513
0008,1060,Name Phys(s) Read Study=1852796513
0008,1070,Operator's Name=anon §  The metadata informaDon is
0008,1080,Admitting Diagnosis Description=1852796513
0008,1090,Manufacturer's Model Name=GENESIS.SIGNA ….. accessible through DICOM tags
0010,0010,Patient's Name=anon
0010,0020,Patient ID=anon
0010,0030,Patient Date of Birth=00000000
0010,0032,Patient Birth Time=000000
0010,0040,Patient Sex=O §  DICOM tags uniquely idenDfy DICOM
0010,1010,Patient Age=000Y
…….. aVributes
0028,0010,Rows=256
0028,0011,Columns=256
0028,0030,Pixel Spacing=0.937500 0.937500

0028,0100,Bits Allocated=16
0028,0101,Bits Stored=16 §  Original data from the scanner tell
0028,0102,High Bit=15
0028,0103,Pixel Representation=1 users important elements about the
…….
7FE0,0010,Pixel Data=131072
acquisiDon
Example of DICOM header content Sonia Pujol PhD, All Rights Reserved 15
Physician and Study
InformaDon
…
0008,0081,City Name=1852796513
0008,0092,?=1852796513
0008,0201,?=-0500
0008,1010,Station Name=1852796513
0008,1070,Operator's Name=anon
0008,1090,Manufacturer's Model Name=GENESIS.SIGNA …..
0010,0040,Patient Sex=O
……..
0028,0010,Rows=256
0028,0011,Columns=256
0028,0030,Pixel Spacing=0.937500 0.937500
0028,0101,Bits Stored=16
0028,0102,High Bit=15
0028,0103,Pixel Representation=1
…….
The Life Cycle of Medical Imaging Data - Sonia Pujol, Ph.D.

Func?onal Magne?c Resonance Imaging: Data Acquisi?on and Analysis Sonia Pujol PhD, All Rights Reserved 16
Harvard-MIT Health Sciences and Technology (HST.583)
PaDent and Study informaDon
…
0008,0081,City Name=1852796513
0008,0092,?=1852796513
0008,0201,?=-0500
0008,1010,Station Name=1852796513
PaDent InformaDon
……..
0028,0010,Rows=256
0028,0011,Columns=256
0028,0030,Pixel Spacing=0.937500 0.937500
0028,0102,High Bit=15
…….

HIPPA PaDent privacy 0002,0000,File Meta Elements Group Len=148
PaDent and Study informaDon
…
The Health Insurance Portability and 0008,0081,City Name=1852796513
Accountability Act of 1996 (HIPAA) protects 0008,0092,?=1852796513

0008,0201,?=-0500
0008,1010,Station Name=1852796513
the privacy and security of certain health 0008,1030,Study Description=anon
informaDon 0008,1050,Performing Physician's Name=1852796513
PaDent InformaDon
hVp://www.hhs.gov/hipaa/index.html 0010,0010,Patient's Name=anon
……..
0028,0010,Rows=256
0028,0011,Columns=256
0028,0030,Pixel Spacing=0.937500 0.937500
0028,0102,High Bit=15
…….

…
0008,0081,City Name=1852796513
0008,0092,?=1852796513
0008,0201,?=-0500
0008,1010,Station Name=1852796513
Image InformaDon
……..
0028,0010,Rows=256
0028,0011,Columns=256
0028,0030,Pixel Spacing=0.937500 0.937500
0028,0102,High Bit=15
…….

…
0008,0081,City Name=1852796513
0008,0092,?=1852796513
0008,0201,?=-0500
0008,1010,Station Name=1852796513
……..
0028,0010,Rows=256
0028,0011,Columns=256
0028,0030,Pixel Spacing=0.937500 0.937500
0028,0102,High Bit=15
Pixel Data
…….

•  DICOM images produced by imaging
equipment: single X-Ray slice , DICOM CT or
DICOM MR volume, DICOM mulD-frame object
(e.g. fMRI experiment, diffusion MRI, DCE)

•  DICOM SegmentaDon Object (SEG):
Examples of
voxels labelled in regions of interest (ROIs)
Standard DICOM

Instances •  DICOM Structured Report (SR):
clinical informaDon (e.g. diagnosis, pathology,
surgery, etc.), measurements computed from
segmented ROIs

Examples of Standard DICOM
Instances
DICOM Images
Prostate MRI Images
DICOM Segmented Structures

mented Structures
Prostate gland, peripheral zone,
lesion, normal Dssue
Measurements
Volumes of prostate gland, peripheral
zone, lesion, normal Dssue
Fedorov et al. Data Descriptor: An annotated test-retest collec?on of mul?parametric MRI. Sci. Data. 2016
22
•  DICOM provides support for segmentaDon
objects and annotaDons

•  DICOM Structured Reports enable
provenance tracking
DICOM Terminology
•  DICOM derived data can be stored on a
DICOM server or on other archive (e.g. TCIA)
with permission, and is compliant with FAIR
principles


DICOM for ArDficial Intelligence
Studies
•  DICOM defines syntax rules and
vocabularies that enable easy
extracDon of knowledge from the data
•  The DICOM framework for medical

imaging data management enables the
automaDon of cohort formaDon and
maximizes the interoperability of the
data for AI studies
Anas et al. MICCAI 2017

Part 2: DICOM and Slicer

•  The Slicer DICOM module provides the
infrastructure for storing, loading and exporDng
DICOM data
•  Slicer supports CT, MRI, PET, X-Ray and

ultrasound DICOM data
Slicer DICOM
module
•  Dedicated Slicer Extensions can be added to
Slicer for imporDng addiDonal DICOM instances
(e.g. DICOM RT Dose, DICOM SegmentaDon
Object, Diffusion Weighted MRI, etc.)

Slicer DICOM
module

DICOM
DICOM data database
loaded into
Slicer
28
DICOM data can be
imported into the Slicer
DICOM database using the
Import DICOM files buVon
or via Drag&Drop
29
PaDents
The DICOM database

follows the DICOM Studies
model hierarchy
organized in paDents,
studies and series
Series
30
The DICOM database se`ngs pannel lets the user choose the
locaDon of the database and enables database maintenance

The DICOM networking pannel
gives access to the DICOM
Listener and DICOM Query/
Retrieve funcDonaliDes of Slicer
(Advanced users)

Part 3: Loading and Visualizing DICOM data in Slicer

Tutorial Dataset
•  Download the SlicerDICOMTutorialData.zip file to your computer
•  Create a SlicerData folder on your computer and move the

SlicerDICOMTutorialData.zip file to the SlicerData folder
•  Unzip the SlicerDICOMTutorialData.zip

Start the 3D Slicer soXware and click on Load DICOM Data
to access the DICOM module
35
Click on DICOM database se`ngs
36
Slicer displays the path to the
default DICOM database locaDon

Click on the default path and change it
to the path of the SlicerData directory
that you created
Dataset #1
Torso CT

Loading a DICOM dataset in Slicer

Drag and drop the directory dataset1_TorsoCT
into the DICOM module
41
Click on paDent1 in
the list of paDents
Slicerdisplays
Slicer displaysthe
the
corresponding
corresponding
studyand
study andseries
series
42
Click on Examine
43
Click on Load
44
The DICOM dataset is loaded into Slicer as
a paDent-study-series DICOM hierarchy
PaDent:
paDent1 (paDent1_ID)
Study:
CT Thorax Abdomen (20050601)
Series:
6: CT_Thorax Abdomen
Instance:
CT Slice
45
Visualizing a DICOM dataset in Slicer

Click on the Slicer GUI icon to
display the list of Slicer layouts
and select ConvenDonal
47
Slicer displays the axial,
coronal and sagiVal images of
6:CT_Thorax_Abdomen series
48
Right-click on 6: CT_Thorax_Abdomen
and select Edit properDes
49
Click on the CT-abdomen preset to
automaDcally adjust the window/level
display of the CT dataset
50
PosiDon the mouse cursor over the red
banner in the Red Viewer to display the
slice menu.

Click on the Links icon to link the slice
controls across all Slice Viewers

Click on the Eye icon to display the three
anatomical slices in the 3D Viewer
51
The three anatomical slices
appear in the 3D viewer
52
Click on the Slicer layout menu icon, and
select ConvenDonal Widescreen layout
53
Slicer switches the layout to
ConvenDonal Widescreen layout
54
Use
Use the
the right
right mouse button in
mouse buVon in the
the
3D
3D Viewer
Viewer to
to zoom
zoom in
out and out
55
Use the leX mouse buVon in the
3D Viewer to rotate the images
56
PosiDon the mouse cursor over
the pin icon in the blue banner
of the 3D viewer window to
display the 3DView controller

Click on the second icon on the
top row of the 3DView controller
to center the 3D view
57
Click on the square icon
next to the leVer ‘R’ to
adjust the field of view
58
Dataset #2
Breast MRI

Breast MRI Dataset
•  The Breast MRI dataset is part of the BREAST-DIAGNOSIS collecDon of
The Cancer Imaging Archive (TCIA) of the NaDonal Cancer InsDtute
•  The dataset was acquired on paDent with right breast infiltraDng
ductal carcinoma
•  The DICOM images consist of one study and three series: T2, STIR and
BLISS
•  BLISS is an MRI sequence for breast MRI studies. BLISS provides the
measurement of two bilateral volumes in a single acquisiDon.

Bloch, B. Nicolas, Jain, Ashali, & Jaffe, C. Carl. (2015). Data From BREAST-DIAGNOSIS. The Cancer Imaging
Archive. hVp://doi.org/10.7937/K9/TCIA.2015.SDNRQXXR

Drag and drop the directory
dataset2_BreastMRI into the DICOM module

Slicer imports the dataset2_BreastMRI directory into
the DICOM database

The directory contains 1 paDent, 1 study and 3 series

Click on the PaDentID
BreastDx-01-0005 to display
the study and the three
T2W, STIR and BLISS series
Click on the double

arrow to display the
list of DICOM readers

The list of DICOM
plugins appear

Slicer DICOM Plugins
•  Slicer implements a list of DICOM
plugins to handle a diverse set of
DICOM data objects
•  These plugins need to be enabled

in order to read specific DICOM
data objects such DICOM RT data
or DICOM DWI data

Sonia Pujol PhD, All Rights Reserved Click on Examine 66
Click on Load to load
the data into Slicer

Slicer loads the three series
of the breast MRI dataset

DICOM data are loaded into Slicer as a
paDent-study-series hierarchy
PaDent:
No name (BreastDx-01-0005)
Study:
MRI BREAST BILATERAL WITH T
WITHOUT CONTRAST (20081111)
Series: Series: Series:

301: T2W_TSE SENSE 401: STIR SENSE AX BLISS AUTO_SENSE
Instance: Instance: Instance:

MR slice MR slice MR slice

Click on the layout menu and
select Yellow slice only

Click on the Adjust window/level
buVon, and use the leX mouse buVon
in the 2D view to adjust the window
and level of the MR images

Click on Play to
playback the series
of BLISS images

Slicer starts playing
the BLISS sequence

Conclusion
•  This tutorial introduced the DICOM standard and
showed how to load and visualize DICOM CT and
MR images in Slicer
•  3D Slicer and the DICOM standard enable
compliance with the FAIR principles for biomedical
research
•  By enabling interoperability between research and
clinical environments, 3D Slicer and the DICOM
standard lower the inherent barriers to the
translaDon of research advances to paDent care

Neuroimaging Analysis Center

Acknowledgments
(NIBIB P41 EB015902)

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DICOM and Slicer:

This tutorial provides a basic introducDon to

Sonia Pujol PhD, All Rights Reserved 2

Part 1: IntroducDon to DICOM

Part 2: DICOM and Slicer

Part 3: Loading and Visualizing DICOM data in Slicer

Sonia Pujol PhD, All Rights Reserved 3

Sonia Pujol PhD, All Rights Reserved 4

Sonia Pujol PhD, All Rights Reserved 6

• Open-source soXware tools such as 3D Slicer and data

Sonia Pujol PhD, All Rights Reserved 7

• Clinical imaging equipment (CT scanners, MR scanners, X-Ray

Sonia Pujol PhD, All Rights Reserved 9

• 1985: PublicaDon of the ACR-NEMA Digital Imaging

• 1993: PublicaDon of the ACR-NEMA Standards

• As of 2020/07/06, the DICOM standard is DICOM

Sonia Pujol PhD, All Rights Reserved

The DICOM Standard facilitates compliance of imaging data

Series Series Series

Sonia Pujol PhD, All Rights Reserved 13

An MRI image is an example of DICOM instance that consists of a DICOM

§ DICOM provides a standardized way

The Life Cycle of Medical Imaging Data - Sonia Pujol, Ph.D.

The Life Cycle of Medical Imaging Data - Sonia Pujol, Ph.D.

Accountability Act of 1996 (HIPAA) protects 0008,0092,?=1852796513

The Life Cycle of Medical Imaging Data - Sonia Pujol, Ph.D.

The Life Cycle of Medical Imaging Data - Sonia Pujol, Ph.D.

The Life Cycle of Medical Imaging Data - Sonia Pujol, Ph.D.

DICOM Segmented Structures

Sonia Pujol PhD, All Rights Reserved 23

• The DICOM framework for medical

Sonia Pujol PhD, All Rights Reserved 24

Sonia Pujol PhD, All Rights Reserved 25

• Slicer supports CT, MRI, PET, X-Ray and

Sonia Pujol PhD, All Rights Reserved 26

Sonia Pujol PhD, All Rights Reserved 27

The DICOM database

Sonia Pujol PhD, All Rights Reserved 31

Sonia Pujol PhD, All Rights Reserved 32

Sonia Pujol PhD, All Rights Reserved 33

• Create a SlicerData folder on your computer and move the

• Unzip the SlicerDICOMTutorialData.zip

Sonia Pujol PhD, All Rights Reserved 34

Sonia Pujol PhD, All Rights Reserved 37

Sonia Pujol PhD, All Rights Reserved 39

Sonia Pujol PhD, All Rights Reserved 40

Sonia Pujol PhD, All Rights Reserved 46

Sonia Pujol PhD, All Rights Reserved 59

Sonia Pujol PhD, All Rights Reserved 60

Sonia Pujol PhD, All Rights Reserved 61

Sonia Pujol PhD, All Rights Reserved 62

Click on the double

Sonia Pujol PhD, All Rights Reserved 63

Sonia Pujol PhD, All Rights Reserved 64

• These plugins need to be enabled

Sonia Pujol PhD, All Rights Reserved 65

Sonia Pujol PhD, All Rights Reserved 67

Sonia Pujol PhD, All Rights Reserved 68

•  Open-source soXware tools such as 3D Slicer and data

•  Clinical imaging equipment (CT scanners, MR scanners, X-Ray

•  1985: PublicaDon of the ACR-NEMA Digital Imaging

•  1993: PublicaDon of the ACR-NEMA Standards

•  As of 2020/07/06, the DICOM standard is DICOM

§  DICOM provides a standardized way

•  The DICOM framework for medical

•  Slicer supports CT, MRI, PET, X-Ray and

•  Create a SlicerData folder on your computer and move the

•  Unzip the SlicerDICOMTutorialData.zip

•  These plugins need to be enabled