CP-2167 Add more brain segmentation labels Status January 2022 Voting Packet Date of Last Update 2021/11/14 Person Assigned David Clunie Submitter Name David Clunie Submission Date 2021/07/24 Correction Number CP-2167 Log Summary: Add more brain segmentation labels Name of Standard PS3.16 Rationale for Correction: Some more labels are needed for labelling the output of neuroimaging tools, some of which are more specific than currently present, and others of which are not actual brain structures but are outputs of the process. For the concept of "Non-brain", have supplied a more generic "Tissue not of interest" concept, which will suffice in context and be reusable for other organs. See, for example: [Ed.Note: CRS Request ID#nnnnn for 301766008; request new codes for FMA 223151] Correction Wording:
Add new Context Group to DICOM PS3.16 as follows:
Anatomically Localized Lesion Segmentation Types Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: yyyymmdd UID: 1.2.840.10008.6.1.uuu1
Anatomically Localized Lesion Segmentation Types
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
SCT 301766008 Lesion of Brain F-A004A C0221505
Amend DICOM PS3.16 as follows:
Brain Structures for Volumetric Measurements Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: 20210328yyyymmdd UID: 1.2.840.10008.6.1.967
Brain Structures for Volumetric Measurements
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
SCT 4958002 Amygdala T-A3230 C0002708
SCT 119238007 Brain Stem T-D0558 C1268144
SCT 11000004 Caudate Nucleus T-A3200 C0007461
SCT 25991003 Cerebellar Cortex T-A6040 C0007759
SCT 33060004 Cerebellar White Matter T-A6080 C0152381
SCT 113305005 Cerebellum T-A6000 C0007765
SCT 40146001 Cerebral Gray Matter T-A2020 C0007776
SCT 68523003 Cerebral White Matter T-A2030 C0152295
SCT 1101003 Cranial Cavity T-D1400 C0230041
SCT 33930006 Cranial Subarachnoid Space T-A1502 C0228145
SCT 74968005 Cavum of septum pellucidum T-A1630 C0228158
SCT 35918002 Fourth Ventricle T-A1820 C0149556
SCT 14738005 Globus Pallidus T-A3500 C0017651
SCT 5366008 Hippocampus T-A2570 C0019564
SCT 263972004 Cerebellar Subarachnoid Space T-A1509 C0446676
SCT 53118009 Inferior Horn of Lateral Ventricle T-A1720 C0152283
SCT 66720007 Lateral Ventricle T-A1650 C0152279
SCT 427667007 Nucleus Accumbens T-A0149 C0028633
SCT 128319008 Intracranial structure T-A0190 C1267697
SCT 89278009 Putamen T-A3400 C0034169
SCT 119406000 Thalamus T-D0593 C0458271
SCT 49841001 Third ventricle T-A1740 C0149555
DCM 110700 Ventral Diencephalon
DCM 110701 White Matter T1 Hypointensity
DCM 110702 White Matter T2 Hyperintensity
(1101003, SCT, "Cranial Cavity") may be used to describe the volume of the entire intra-cranial space (intra-cranial volume or ICV) though the coded concept used is "structure of" rather than "entire" to be consistent with normal DICOM practice. (25991003, SCT, "Cerebellar Cortex") is the gray matter of the cerebellum (as distinct from (33060004, SCT, "Cerebellar white matter")). (33930006, SCT, "Cranial Subarachnoid Space") may be used to describe the volume of the exterior CSF (surrounding the brain, excluding the ventricles). (263972004, SCT, "Cerebellar Subarachnoid Space") may be used to describe the volume of the inferior intracranial CSF space (infra-tentorial).
CNS Segmentation Types Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: 20200309yyyymmdd UID: 1.2.840.10008.6.1.499
CNS Segmentation Types
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
SCT 62818001 Adenohypophysis T-B1100 C0032008
SCT 4958002 Amygdala T-A3230 C0002708
SCT 75042008 Arachnoid T-A1220 C0003707
FMA 276650 Arcuate Fasciculus C2329633
SCT 12738006 Brain T-A0100 C0006104
SCT 280371009 Brain cerebrospinal fluid pathway T-A0109 C0459387
SCT 119238007 Brain stem T-D0558 C1268144
SCT 35764002 Brain ventricle T-A1600 C0007799
SCT 11000004 Caudate nucleus T-A3200 C0007461
SCT 21483005 Central nervous system T-A0090 C0927232
SCT 33060004 Cerebellar white matter T-A6080 C0152381
SCT 113305005 Cerebellum T-A6000 C0007765
SCT 80447000 Cerebral aqueduct T-A1800 C0007769
SCT 40146001 Cerebral cortex T-A2020 C0007776
SCT 87463005 Cerebral fornix T-A2970 C0152334
SCT 40146001 Cerebral Gray Matter T-A2020 C0007776
SCT 372073000 Cerebral hemisphere T-A010F
SCT 68523003 Cerebral White Matter T-A2030 C0152295
SCT 65216001 Cerebrospinal Fluid T-A1000 C0007806
SCT 37035000 Cingulum T-A2840 C0228272
SCT 88442005 Corpus callosum T-A2700 C0010090
SCT 31428008 Corpus striatum T-A3100 C0010097
SCT 87563008 Diencephalon T-A0102 C0012144
SCT 18545000 Dura mater T-A1120 C0013313
SCT 3937002 Entorhinal Cortex T-A2594 C0175196
SCT 35918002 Fourth ventricle T-A1820 C0149556
SCT 83251001 Frontal lobe T-A2200 C0016733
SCT 14738005 Globus pallidus T-A3500 C0017651
SCT 389081007 Gray Matter T-A0096 C1300312
SCT 5366008 Hippocampus T-A2570 C0019564
SCT 67701001 Inferior cerebellar peduncle T-A6640 C0152393
SCT 55233005 Inferior longitudinal fasciculus T-A2850 C0228273
SCT 36169008 Insula T-A2610 C0021640
SCT 461002 Lateral corticospinal tract T-A7093 C0152402
SCT 66720007 Lateral ventricle T-A1650 C0152279
SCT 279215006 Limbic lobe T-A0036 C0458337
SCT 30114003 Medial Lemniscus T-A5271 C0228420
SCT 1231004 Meninges T-A1110 C0025285
SCT 61962009 Midbrain T-A5100 C0025462
SCT 33723005 Middle cerebellar peduncle T-A6630 C0152392
SCT 427667007 Nucleus accumbens T-A0149 C0028633
SCT 37512009 Neurohypophysis T-B1200 C0032009
SCT 31065004 Occipital lobe T-A2400 C0028785
SCT 244453006 Optic chiasm T-A800B C0029126
SCT 70105001 Optic radiation T-A2880 C0228277
SCT 53238003 Optic tract T-A8060 C0152405
SCT 16630005 Parietal lobe T-A2300 C0030560
SCT 23180006 Pia mater T-A1280 C0031869
SCT 45793000 Pineal Gland T-B2000 C0031939
SCT 56329008 Pituitary T-B1000 C0032005
SCT 279336005 Posterior cerebral commissure T-A4904 C0152327
SCT 89278009 Putamen T-A3400 C0034169
SCT 280401006 Spinal cerebrospinal fluid pathway T-D0721 C0459413
SCT 2748008 Spinal cord T-A7010 C0037925
SCT 12958003 Spinal cord gray matter T-A7020 C0475853
SCT 27088001 Spinal cord white matter T-A7070 C0458457
SCT 35951006 Subarachnoid space T-A1500 C0038527
FMA 223151 Subcortical gray matter C2333161
SCT 70007007 Substantia nigra T-A5160 C0038590
SCT 11089000 Superior cerebellar peduncle T-A6620 C0152391
SCT 89202009 Superior longitudinal fasciculus T-A2820 C0228270
SCT 11628009 Telencephalon T-A0103 C0039452
SCT 78277001 Temporal lobe T-A2500 C0039485
SCT 42695009 Thalamus T-A4000 C0039729
SCT 49841001 Third ventricle T-A1740 C0149555
SCT 26230003 Uncinate fasciculus T-A2830 C0228271
SCT 389080008 White Matter T-A0095 C1300311
Lesion Segmentation Types Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: 20210328 UID: 1.2.840.10008.6.1.505
Lesion Segmentation Types
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
SCT 44132006 Abscess M-41610 C0000833
SCT 75753009 Blood clot M-35000 C0302148
SCT 367643001 Cyst M-3340A C0010709
SCT 79654002 Edema M-36300 C0013604
SCT 55584005 Embolus M-35300 C1704212
SCT 50960005 Hemorrhage M-37000 C0019080
SCT 409774005 Inflammation M-0100C C1444073
SCT 52988006 Lesion M-01100 C0221198
SCT 4147007 Mass M-03000 C0577559
SCT 6574001 Necrosis M-54000 C0027540
SCT 108369006 Neoplasm M-8FFFF C0027651
SCT 86049000 Neoplasm, Primary M-80003 C1306459
SCT 14799000 Neoplasm, Secondary M-80006 C2939419
SCT 27925004 Nodule M-03010 C0028259
Include
Abstract Segmentation Types Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: 20190327yyyymmdd UID: 1.2.840.10008.6.1.962
Abstract Segmentation Types
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
DCM 125040 Background
SCT 85756007 Tissue T-D0050 C0040300
DCM ddd001 Tissue not of interest
SCT 289925000 Waste Material F-61779 C0043045
DCM 125041 Registration Input
DCM 113132 Single subject extracted from group
NCIt C94970 Reference Region C2986814
SCT 17621005 Normal G-A460 C0205307
The concept (17621005, SCT, "Normal") is a general normality qualifier used here to mean normal in the context of the structural or functional image being segmented, whether it be "normal tissue" or "normal function". Normal may be distinguished from background (e.g., where there is no tissue at all).
Common Tissue Segmentation Types Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: 20200921 UID: 1.2.840.10008.6.1.963
Common Tissue Segmentation Types
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
SCT 51114001 Artery T-41000 C0003842
SCT 87612001 Blood T-C2000 C0005767
SCT 59820001 Blood vessel T-40000 C0005847
SCT 248300009 Body fat F-03D38 C0344335
SCT 272673000 Bone T-D016E C0262950
SCT 20982000 Capillary T-40050 C0006901
SCT 309312004 Cartilage T-D021B C0007301
SCT 21793004 Connective tissue T-1A200 C0009780
SCT 52082005 Ligament T-18010 C0023685
SCT 59441001 Lymph node T-C4000 C0024204
SCT 89890002 Lymphatic system T-C6000 C0024235
SCT 83555006 Lymphatic vessel T-C6010 C0229889
SCT 74135004 Meniscus T-15009 C0224498
SCT 71616004 Muscle T-13001 C0026845
SCT 119410002 Nerve T-D0598 C1268169
SCT 113343008 Organ T-D0060 C0229983
SCT 39937001 Skin T-01000 C1123023
SCT 87784001 Soft tissue T-1A000 C0225317
SCT 71966008 Subcutaneous tissue T-03000 C0278403
SCT 13024002 Tendon T-17010 C0039508
SCT 85756007 Tissue T-D0050 C0040300
SCT 29092000 Vein T-48000 C0042449
Blood and body fat are considered tissues rather than body substances because they are cellular.
Brain Lesion Segmentation Types With Necrosis Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: 20190327 UID: 1.2.840.10008.6.1.1280
Brain Lesion Segmentation Types With Necrosis
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
Include
SCT 6574001 Necrosis M-54000 C0027540
The same concept for non-enhancing tumor is used in this Context Group and when included in . When used in this Context Group, non-enhancing tumor excludes any necrotic region, whereas when used in , it does not.
Brain Lesion Segmentation Types Without Necrosis Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: 20190327 UID: 1.2.840.10008.6.1.1281
Brain Lesion Segmentation Types Without Necrosis
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
DCM 125040 Background
SCT 17621005 Normal G-A460 C0205307
SCT 79654002 Edema M-36300 C0013604
NCIt C81175 Non-Enhancing Lesion C2825493
NCIt C113842 Enhancing Lesion C3830314
The concept (17621005, SCT, "Normal") is a general normality qualifier used here in context to mean normally appearing brain tissue on an imaging study. Some coding schemes contain more specific concepts such as "normal tissue" (but may be part of a coding scheme for histopathology rather than imaging) or "normal brain" or "normal white matter". Normal may be distinguished from background (e.g., where there is no tissue at all). A generic concept for edema is used for consistency with other segmentation-related Context Groups, rather than a more specific anatomy or tumor-related concept such as (C121674, NCIt , "Peritumoral Brain Edema") UMLS:C4054192. The same concept for non-enhancing tumor is used in this Context Group and when included in . When used in this Context Group, non-enhancing tumor includes any necrotic region, whereas when used in , it does not.
Morphologically Abnormal Structure Segmentation Property Types Resources: HTML | FHIR JSON | FHIR XML | IHE SVS XML Type: Extensible Version: 20170914yyyymmdd UID: 1.2.840.10008.6.1.1193
Morphologically Abnormal Structure Segmentation Property Types
Coding Scheme Designator Code Value Code Meaning SNOMED-RT ID UMLS Concept Unique ID
Include
Include
DICOM Controlled Terminology Definitions (Normative)
DICOM Controlled Terminology Definitions (Coding Scheme Designator "DCM" Coding Scheme Version "01")
Code Value Code Meaning Definition Notes
125040 Background That which is not part of an object. E.g., background of an image (that which might be encoded with Pixel Padding Value, or a Segmentation Property Type.
ddd001 Tissue not of interest Tissue that is other than that of interest for the purpose of the task. E.g., segmented non-brain tissue in an image where the primary purpose is to segment the brain and/or its structure, and non-brain tissue that is distinct from background needs to be identified.
Add new Context Group UIDs to DICOM PS3.6 as follows:
Context Group UID Values
Context UID Context Identifier Context Group Name Comment
1.2.840.10008.6.​1.​uuu1