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Determining Scanned Body Part from DICOM Study Description for Relevant Prior Study Matching
Thusitha Mabotuwana, Yuechen Qian Philips Research North America 21 August 2013
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Typical radiology workflow
Imaging order (fax/e-referral) HL7 HL7 Exam Protocoling HL7
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Typical radiology workflow
DICOM Imaging order (fax/e-referral) DICOM HL7 Reporting HL7 Exam Protocoling HL7
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Typical radiology workflow
DICOM Imaging order (fax/e-referral) HL7 Reporting DICOM HL7 Exam Protocoling HL7
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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.
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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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Overview Clinical need Technical challenges Our solution Validation
Discussion
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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”
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A typical DICOM header
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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 Study Description CT ABDOMEN CT ABDOMEN WITH CONT SPLEEN CT NEEDLE BIOPSY LIVER RF XR PERITONEOGRAM US US PORT RENAL LTD CT ABDOMEN W/O KIDNEYS CT ABDOMEN WO PANCREAS MRI BONE MRI ANKLE/FOOT W RT XR KNEE ARTHROGRAM RT CR XR PORT ANKLE 2 VIEWS LT CARDIAC CT HEART W/WO GAIT 3D CNT FNC EVL CHEST CT ANGIO CARDIAC WWO GI XR UGI W KUB XC GIEC COLON NEURO MRI P PITUITARY WO US PORT NECK THYROID/SOFT TISSUE Can an algorithm be developed to reliably extract the most specific anatomy information from DICOM Study Description field?
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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
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Algorithm development – reference taxonomy
- 160 unique concepts were included in the taxonomy with an additional 87 terms included as synonyms or abbreviations RadLex/Snomed can be used for reasoning if needed
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Algorithm development – reference taxonomy features
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’). 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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Input string MRI ANKLE/FOOT WWO LT Empty or null string Return
Remove stop words and special characters; convert to lower case mri ankle foot lt Replace known global abbreviations (e.g., LT with left) mri ankle foot 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 Yes left foot left ankle Empty input string or all combinations processed Yes Intelligent filtering Show children concepts? No left foot No Process next word combination Yes Match found? Add matched term to list No All combinations for current iteration finished? Yes Replace matched terms from input string No
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Input string MRI ANKLE/FOOT WWO LT Empty or null string Return
Remove stop words and special characters; convert to lower case mri ankle foot lt Replace known global abbreviations (e.g., LT with left) mri ankle foot 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 Yes left foot left ankle Empty input string or all combinations processed Yes Intelligent filtering Show children concepts? No left foot No Process next word combination Yes Match found? Add matched term to list No All combinations for current iteration finished? Yes Replace matched terms from input string No
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Input string MRI ANKLE/FOOT WWO LT Empty or null string Return
Remove stop words and special characters; convert to lower case mri ankle foot lt Replace known global abbreviations (e.g., LT with left) mri ankle foot 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 Yes left foot left ankle Empty input string or all combinations processed Yes Intelligent filtering Show children concepts? No left foot No Process next word combination Yes Match found? Add matched term to list No All combinations for current iteration finished? Yes Replace matched terms from input string No
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Input string MRI ANKLE/FOOT WWO LT Empty or null string Return
Remove stop words and special characters; convert to lower case mri ankle foot lt Replace known global abbreviations (e.g., LT with left) mri ankle foot 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 Yes left foot left ankle Empty input string or all combinations processed Yes Intelligent filtering Show children concepts? No left foot No Process next word combination Yes Match found? Add matched term to list No All combinations for current iteration finished? Yes Replace matched terms from input string No
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Input string MRI ANKLE/FOOT WWO LT Empty or null string Return
Remove stop words and special characters; convert to lower case mri ankle foot lt Replace known global abbreviations (e.g., LT with left) mri ankle foot 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 Yes left foot left ankle Empty input string or all combinations processed Yes Intelligent filtering Show children concepts? No left foot No Process next word combination Yes Match found? Add matched term to list No All combinations for current iteration finished? Yes Replace matched terms from input string No
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Input string MRI ANKLE/FOOT WWO LT Empty or null string Return
Remove stop words and special characters; convert to lower case mri ankle foot lt Regex based anatomy extraction: (?=.*\bank).*(?=.*\bfoo).*(?=.*\blef).* Replace known global abbreviations (e.g., LT with left) mri ankle foot 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 Yes left foot left ankle Empty input string or all combinations processed Yes Intelligent filtering Show children concepts? No left foot No Process next word combination Yes Match found? Add matched term to list No All combinations for current iteration finished? Yes Replace matched terms from input string No
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Input string MRI ANKLE/FOOT WWO LT Empty or null string Return
Remove stop words and special characters; convert to lower case mri ankle foot lt Replace known global abbreviations (e.g., LT with left) mri ankle foot 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 Yes left foot left ankle Empty input string or all combinations processed Yes Intelligent filtering Show children concepts? No left foot No Process next word combination Yes Match found? Add matched term to list No All combinations for current iteration finished? Yes Replace matched terms from input string No
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Input string MRI ANKLE/FOOT WWO LT Empty or null string Return
Remove stop words and special characters; convert to lower case mri ankle foot lt Replace known global abbreviations (e.g., LT with left) mri ankle foot 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 Yes left foot left ankle Empty input string or all combinations processed Yes Intelligent filtering Show children concepts? No left foot No Process next word combination Yes Match found? Add matched term to list No All combinations for current iteration finished? Yes Replace matched terms from input string No
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Input string MRI ANKLE/FOOT WWO LT Empty or null string Return
Remove stop words and special characters; convert to lower case mri ankle foot lt Replace known global abbreviations (e.g., LT with left) mri ankle foot 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 Yes left foot left ankle Empty input string or all combinations processed Yes Intelligent filtering Show children concepts? No left foot No Process next word combination Yes Match found? Add matched term to list No All combinations for current iteration finished? Yes Replace matched terms from input string No
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Input string MRI ANKLE/FOOT WWO LT Empty or null string Return
Remove stop words and special characters; convert to lower case mri ankle foot lt Replace known global abbreviations (e.g., LT with left) mri ankle foot 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 Yes left foot left ankle Empty input string or all combinations processed Yes Intelligent filtering Show children concepts? No left foot No Process next word combination Yes Match found? Add matched term to list No All combinations for current iteration finished? Yes Replace matched terms from input string No
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Input string MRI ANKLE/FOOT WWO LT Empty or null string Return
Remove stop words and special characters; convert to lower case mri ankle foot lt Replace known global abbreviations (e.g., LT with left) mri ankle foot 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 Yes left foot left ankle Empty input string or all combinations processed Yes Intelligent filtering Show children concepts? No left foot No Process next word combination Yes Match found? Add matched term to list No All combinations for current iteration finished? Yes Replace matched terms from input string No
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Algorithm validation Extracted 1604 production study descriptions from an academic institution Used 1200 (~80%) for algorithm development 404 used for testing Accuracy of system was 99.94%. (XR SACRUM COCCYX 2 VIEWS MIN was the false-negative) Body part extracted Ground Truth (n=1200) True False 1057 143 Body part extracted Ground Truth (n=404) True False 197 1 206
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Results Study Description Extracted Body Part Category
CT ABDOMEN WITH CONT SPLEEN Spleen Direct match CT NEEDLE BIOPSY LIVER Liver CT HEART W/WO GAIT 3D Heart CT ABDOMEN W/O KIDNEYS Kidney CT ABDOMEN W/O PANCREAS Pancreas GIEC COLON Colon MRI P PITUITARY WO Pituitary MRI ANKLE/FOOT W RT Right ankle, right foot Direct match + laterality XR KNEE ARTHROGRAM RT Right knee XR PORT ANKLE 2 VIEWS LT Left ankle US PORT NECK THYROID/SOFT TISSUE Neck, thyroid soft tissue Direct match + post processing XR PERITONEOGRAM Peritoneum Procedure POSITRON EMISSION MAMMOGRAPHY Breast US PORT RENAL LTD Synonym XR UGI W KUB Upper gastrointestinal tract 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
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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.
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Questions? Thusitha Mabotuwana
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