Projects:QIN:3D Slicer Annotation Image Markup:Standard Terminology

This is a collection of relevant pieces from:

• http://medical.nema.org/Dicom/2011/11_03pu.pdf
• http://medical.nema.org/Dicom/2011/11_16pu.pdf

Segmentation image module attributes

Segmentation image module attributes must in particular include the following (PS 3.3-2011, p.989):

Code sequence attributes

General Anatomy Macro

The General Anatomy Macro is defined as follows (PS 3.3-2011, p.96):

Coding Scheme Designators

NOTE: this table is incomplete, consult PS 3.16-2011 p.43.

RadLex

• General information: http://rsna.org/RadLex.aspx
• License: http://rsna.org/uploadedFiles/RSNA/Content/Informatics/radlex_public_license_version_1-0-1.pdf
• Example hierarchy of the term mapping from RadLex browser (liver: http://www.radlex.org/RID/RID13419):

SNOMED

David Clunie in email communication Sept 17, 2012:

[...] The [DICOM] agreement with SNOMED
is to allow any implementer to use the terms included in DICOM in their
implementations and products without fee; it is not just to be able to
include them in the text of the standard documents.

So, since Slicer would be using the concepts to include in a DICOM SEG
object, you do not need any additional agreement, nor any agreement with
SNOMED to distribute the source code (my PixelMed Java DICOM toolkit is
full of SNOMED codes, for example, and I neither have not need such an
additional agreement).

Notes on choosing SNOMED concepts when fleshing out the table, esp. regarding anatomy. Make sure that you choose "(body structure)" concepts for anatomy, and that you pick the "entire ..." concept rather than "structure of" etc., and if the choice is not obvious, include about your choice so that these can be flagged for special attention during review.

One way to find the right SNOMED code without using one of the terminology browsers is just to download the text files from the UMLS (from http://www.nlm.nih.gov/research/umls/licensedcontent/snomedctfiles.html). You will need to register and get a user name and password.

Then you can use grep as follows:

% grep -i 'frontal lobe' sct1_Concepts_Core_INT_20110131.txt | grep -i structure | grep -i entire
180920004	0	Entire frontal lobe (body structure)	7N000	T-A2218	1
279169003	0	Entire frontal lobe gyrus (body structure)	Xa10B	T-A2207	1
314141005	0	Entire right frontal lobe (body structure)	XaEYz	T-A2213	0
314142003	0	Entire left frontal lobe (body structure)	XaEZ0	T-A2214	0
362330001	0	Entire cortex of frontal lobe (body structure)	XU96w	T-A2211	1
362331002	0	Entire white matter of frontal lobe (body structure)	XU96y	T-A2221	1

You can find this sort of thing using the UMLS Terminology Browser (at https://uts.nlm.nih.gov/metathesaurus.html), for example, as follows:

Mapping Slicer GeneralAnatomy LUT to SNOMED Standard Terminology

Original GeneralAnatomy LUT is available here: https://www.slicer.org/wiki/Documentation/4.1/SlicerApplication/LookupTables/GenericAnatomyColors. The table mapping was compiled by David Clunie, Andrey Fedorov and Neha Agrawal to include Segmented Property Category, Type and Modifier (when appropriate), which are required for encoding label segments in DICOM SEG. See Reporting module documentation for the most up to date mapping.

Licensing and redistribution: per agreement between SNOMED and DICOM, "the agreement with SNOMED is to allow any implementer to use the terms included in DICOM in their implementations and products without fee". DICOM correction proposal CP-1528 (ftp://medical.nema.org/medical/dicom/cp/cp1258_01.pdf, Refactor segment description, extend segment types and anatomy) contains the items included in this table.