Determining Scanned Body Part from
DICOM Study Description for Relevant
Prior Study Matching
Thusitha Mabotuwana, Yuechen Qian
Philips Research North America
21 August 2013
Typical radiology workflow
Imaging order
(fax/e-referral)
HL7
HL7
HL7
Exam Protocoling
2
Typical radiology workflow
Imaging order
(fax/e-referral)
DICOM
HL7
Reporting
DICOM
HL7
HL7
Exam Protocoling
3
Typical radiology workflow
Imaging order
(fax/e-referral)
DICOM
HL7
Reporting
DICOM
HL7
HL7
Exam Protocoling
4
Background
• Radiologists need to understand the clinical context when reading a new
study.
• Most relevant prior study is often used as the reference to compare
current findings against.
Current status
- Important to find the correct prior study for comparison.
- Determining relevant prior study is not always straight-forward, especially
with complex patients having many (e.g., >20) studies for multiple conditions.
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Current status – opportunity for improvement
- Typically, matching is done based on scanned body part (e.g., Head,
Abdomen) corresponding to Body Part Examined field in DICOM (0018, 0015)
- Body part field of the DICOM header is fairly generic
- e.g., Study done to exclude pancreatitis and another study done to
exclude renal stones will both have their body part field set to
“abdomen”
8
A typical DICOM header
9
Our approach
Identified other DICOM attributes containing anatomy related information.
- DICOM Study Description (0008, 1030) field
- e.g., CT CHEST ABD/PEL LIVER
- DICOM Protocol Name (0018, 1030) field
- e.g., C/A/P W/ARTERIAL LIVER/Abdomen
- DICOM Series Description(0008, 103e) field
- e.g., LUNGS, Coronal
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DICOM Study Description field
Narrative, free-text and institution-specific terms (i.e., non-standardized).
- Abbreviations (e.g., UE – upper extremity)
- Synonyms (e.g., neuro)
- Procedure names (e.g., mammogram)
Modality
Body Part
Examined
CT
CT
RF
US
CT
CT
MRI
RF
CR
CT
CT
RF
XC
ABDOMEN
ABDOMEN
ABDOMEN
ABDOMEN
ABDOMEN
ABDOMEN
BONE
BONE
BONE
CARDIAC
CHEST
GI
GI
MRI
US
NEURO
NEURO
Study Description
CT ABDOMEN WITH CONT SPLEEN
CT NEEDLE BIOPSY LIVER
XR PERITONEOGRAM
US PORT RENAL LTD
CT ABDOMEN W/O KIDNEYS
CT ABDOMEN WO PANCREAS
MRI ANKLE/FOOT W RT
XR KNEE ARTHROGRAM RT
XR PORT ANKLE 2 VIEWS LT
CT HEART W/WO GAIT 3D CNT FNC EVL
CT ANGIO CARDIAC WWO
XR UGI W KUB
GIEC COLON
MRI P PITUITARY WO
US PORT NECK THYROID/SOFT TISSUE
- Can an algorithm be developed to reliably extract the most specific anatomy
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information from DICOM Study Description field?
System overview
Preprocessing (e.g., stop word removal)
Word normalization (e.g., global abbreviation replacement – ‘LT’)
Procedure-related anatomy extraction (e.g., mammogram)
Anatomy extraction using word combinations
Postprocessing of extracted anatomies
12
Algorithm development – reference taxonomy
- 160 unique concepts were included in the taxonomy with an additional 87
terms included as synonyms or abbreviations
13
Algorithm development – reference taxonomy
features
1.
2.
3.
4.
Parent-child relationship between concepts.
Multiple abbreviations and/or synonyms.
Child concepts inherit properties from parents (e.g., laterality)
Concepts should be interpreted within the context of its ancestor (e.g.,
‘soft tissues’ may appear multiple times in the taxonomy, but MRI P FACE
SOFT TISSUE W would match to ‘face soft tissues’).
5. The taxonomy is a representation of intention of procedure (e.g., a
mammogram study description – MAM BILAT DIGITAL W/CAD does not
explicitly mention ‘breast’).
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MRI ANKLE/FOOT WWO LT
Input string
Empty or null string
mri ankle foot lt
Remove stop words and special
characters; convert to lower case
mri ankle foot left
Replace known global
abbreviations (e.g., LT with left)
ankle foot left
Determine modality and replace
i) ankle foot left
ii) ankle foot
foot left
ankle left
Determine word combinations for
input string in descending order
Empty input string or all
combinations processed
Return
Yes
Yes
Intelligent
filtering
Show children
concepts?
left foot
left ankle
No
left foot
No
Process next word combination
Yes
Match found?
Add matched term to list
No
All combinations for current
iteration finished?
No
Yes
Replace matched terms
from input string
15
MRI ANKLE/FOOT WWO LT
Input string
Empty or null string
mri ankle foot lt
Remove stop words and special
characters; convert to lower case
mri ankle foot left
Replace known global
abbreviations (e.g., LT with left)
ankle foot left
Determine modality and replace
i) ankle foot left
ii) ankle foot
foot left
ankle left
Determine word combinations for
input string in descending order
Empty input string or all
combinations processed
Return
Yes
Yes
Intelligent
filtering
Show children
concepts?
left foot
left ankle
No
left foot
No
Process next word combination
Yes
Match found?
Add matched term to list
No
All combinations for current
iteration finished?
No
Yes
Replace matched terms
from input string
16
MRI ANKLE/FOOT WWO LT
Input string
Empty or null string
mri ankle foot lt
Remove stop words and special
characters; convert to lower case
mri ankle foot left
Replace known global
abbreviations (e.g., LT with left)
ankle foot left
Determine modality and replace
i) ankle foot left
ii) ankle foot
foot left
ankle left
Determine word combinations for
input string in descending order
Empty input string or all
combinations processed
Return
Yes
Yes
Intelligent
filtering
Show children
concepts?
left foot
left ankle
No
left foot
No
Process next word combination
Yes
Match found?
Add matched term to list
No
All combinations for current
iteration finished?
No
Yes
Replace matched terms
from input string
17
MRI ANKLE/FOOT WWO LT
Input string
Empty or null string
mri ankle foot lt
Remove stop words and special
characters; convert to lower case
mri ankle foot left
Replace known global
abbreviations (e.g., LT with left)
ankle foot left
Determine modality and replace
i) ankle foot left
ii) ankle foot
foot left
ankle left
Determine word combinations for
input string in descending order
Empty input string or all
combinations processed
Return
Yes
Yes
Intelligent
filtering
Show children
concepts?
left foot
left ankle
No
left foot
No
Process next word combination
Yes
Match found?
Add matched term to list
No
All combinations for current
iteration finished?
No
Yes
Replace matched terms
from input string
18
MRI ANKLE/FOOT WWO LT
Input string
Empty or null string
mri ankle foot lt
Remove stop words and special
characters; convert to lower case
mri ankle foot left
Replace known global
abbreviations (e.g., LT with left)
ankle foot left
Determine modality and replace
i) ankle foot left
ii) ankle foot
foot left
ankle left
Determine word combinations for
input string in descending order
Empty input string or all
combinations processed
Return
Yes
Yes
Intelligent
filtering
Show children
concepts?
left foot
left ankle
No
left foot
No
Process next word combination
Yes
Match found?
Add matched term to list
No
All combinations for current
iteration finished?
No
Yes
Replace matched terms
from input string
19
MRI ANKLE/FOOT WWO LT
mri ankle foot lt
mri ankle foot left
Input string
Empty or null string
Return
Remove stop words and special
characters; convert to lower case
Regex based anatomy extraction:
(?=.*\bank).*(?=.*\bfoo).*(?=.*\blef).*
Replace known global
abbreviations (e.g., LT with left)
ankle foot left
Determine modality and replace
i) ankle foot left
ii) ankle foot
foot left
ankle left
Determine word combinations for
input string in descending order
Empty input string or all
combinations processed
Yes
Yes
Intelligent
filtering
Show children
concepts?
left foot
left ankle
No
left foot
No
Process next word combination
Yes
Match found?
Add matched term to list
No
All combinations for current
iteration finished?
No
Yes
Replace matched terms
from input string
20
MRI ANKLE/FOOT WWO LT
Input string
Empty or null string
mri ankle foot lt
Remove stop words and special
characters; convert to lower case
mri ankle foot left
Replace known global
abbreviations (e.g., LT with left)
ankle foot left
Determine modality and replace
i) ankle foot left
ii) ankle foot
foot left
ankle left
Determine word combinations for
input string in descending order
Empty input string or all
combinations processed
Return
Yes
Yes
Intelligent
filtering
Show children
concepts?
left foot
left ankle
No
left foot
No
Process next word combination
Yes
Match found?
Add matched term to list
No
All combinations for current
iteration finished?
No
Yes
Replace matched terms
from input string
21
MRI ANKLE/FOOT WWO LT
Input string
Empty or null string
mri ankle foot lt
Remove stop words and special
characters; convert to lower case
mri ankle foot left
Replace known global
abbreviations (e.g., LT with left)
ankle foot left
Determine modality and replace
i) ankle foot left
ii) ankle foot
foot left
ankle left
Determine word combinations for
input string in descending order
Empty input string or all
combinations processed
Return
Yes
Yes
Intelligent
filtering
Show children
concepts?
left foot
left ankle
No
left foot
No
Process next word combination
Yes
Match found?
Add matched term to list
No
All combinations for current
iteration finished?
No
Yes
Replace matched terms
from input string
22
MRI ANKLE/FOOT WWO LT
Input string
Empty or null string
mri ankle foot lt
Remove stop words and special
characters; convert to lower case
mri ankle foot left
Replace known global
abbreviations (e.g., LT with left)
ankle foot left
Determine modality and replace
i) ankle foot left
ii) ankle foot
foot left
ankle left
Determine word combinations for
input string in descending order
Empty input string or all
combinations processed
Return
Yes
Yes
Intelligent
filtering
Show children
concepts?
left foot
left ankle
No
left foot
No
Process next word combination
Yes
Match found?
Add matched term to list
No
All combinations for current
iteration finished?
No
Yes
Replace matched terms
from input string
23
MRI ANKLE/FOOT WWO LT
Input string
Empty or null string
mri ankle foot lt
Remove stop words and special
characters; convert to lower case
mri ankle foot left
Replace known global
abbreviations (e.g., LT with left)
ankle foot left
Determine modality and replace
i) ankle foot left
ii) ankle foot
foot left
ankle left
Determine word combinations for
input string in descending order
Empty input string or all
combinations processed
Return
Yes
Yes
Intelligent
filtering
Show children
concepts?
left foot
left ankle
No
left foot
No
Process next word combination
Yes
Match found?
Add matched term to list
No
All combinations for current
iteration finished?
No
Yes
Replace matched terms
from input string
24
MRI ANKLE/FOOT WWO LT
Input string
Empty or null string
mri ankle foot lt
Remove stop words and special
characters; convert to lower case
mri ankle foot left
Replace known global
abbreviations (e.g., LT with left)
ankle foot left
Determine modality and replace
i) ankle foot left
ii) ankle foot
foot left
ankle left
Determine word combinations for
input string in descending order
Empty input string or all
combinations processed
Return
Yes
Yes
Intelligent
filtering
Show children
concepts?
left foot
left ankle
No
left foot
No
Process next word combination
Yes
Match found?
Add matched term to list
No
All combinations for current
iteration finished?
No
Yes
Replace matched terms
from input string
25
Algorithm validation
- Extracted 1604 production study descriptions from an academic institution
- Used 1200 (~80%) for algorithm development
Ground Truth (n=1200)
Body part extracted
True
False
True
1057
0
False
0
143
- 404 used for testing
Ground Truth (n=404)
Body part extracted
True
False
True
197
0
False
1
206
- Accuracy of system was 99.94%.
-
(XR SACRUM COCCYX 2 VIEWS MIN was the false-negative)
Results
Study Description
CT ABDOMEN WITH CONT SPLEEN
CT NEEDLE BIOPSY LIVER
CT HEART W/WO GAIT 3D
CT ABDOMEN W/O KIDNEYS
CT ABDOMEN W/O PANCREAS
GIEC COLON
MRI P PITUITARY WO
MRI ANKLE/FOOT W RT
XR KNEE ARTHROGRAM RT
XR PORT ANKLE 2 VIEWS LT
US PORT NECK THYROID/SOFT TISSUE
XR PERITONEOGRAM
POSITRON EMISSION MAMMOGRAPHY
US PORT RENAL LTD
XR UGI W KUB
Extracted Body Part
Category
Spleen
Liver
Heart
Kidney
Pancreas
Colon
Pituitary
Right ankle, right foot
Right knee
Left ankle
Neck, thyroid soft tissue
Peritoneum
Breast
Kidney
Upper gastrointestinal tract
Direct match
Direct match
Direct match
Direct match
Direct match
Direct match
Direct match
Direct match + laterality
Direct match + laterality
Direct match + laterality
Direct match + post processing
Procedure
Procedure
Synonym
Abbreviation
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Limitations
- Dataset is from one institution and therefore abbreviations and algorithms
may need to be generalizable across institutions.
- The reference taxonomy is not complete and represents only concepts
encountered in the training set, as well as those included based on authors’
domain experience
Key messages
- Knowing the most specific body part of an imaging study is important for
relevant prior study matching.
- A regular expression based technique can be used to extract specific anatomy
information from DICOM Study Description.
Questions?
Thusitha Mabotuwana
thusitha.mabotuwana@philips.com
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