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

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This is a collection of relevant pieces from:

Segmentation image module attributes

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

PS3.3-SegmentationAttributes.png

PS3.3-CodedEntryData.png

Code sequence attributes

PS3.3-CodeSequenceAttributes.png

General Anatomy Macro

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

PS3.3-GeneralAnatomyMacro.png

Coding Scheme Designators

PS3.3-CodingSchemeDesignators1.png

PS3.3-CodingSchemeDesignators2.png

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

RadLex

RadLex RID13419.png

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).

Mapping Slicer GeneralAnatomy LUT to Standard Terminology (work in progress)

Original GeneralAnatomy LUT see here: http://www.slicer.org/slicerWiki/index.php/Slicer3:2010_GenericAnatomyColors

Original labels categorized

integer_label text_label color notes anatomic region anatomic region modifier primary anatomic structure primary anatomic structure modifier segmented property category - CID 7150 segmented property type segmented property type modifier
0 background rgba(0,0,0,0)
1 tissue rgb(128,174,128) Default label for bodily tissues (T-D0050,SRT,"Tissue")
2 bone rgb(241,214,145) (T-D0050,SRT,"Tissue") (T-D016E,SRT,"Bone")
3 skin rgb(177,122,101)
4 connective tissue rgb(111,184,210)
5 blood rgb(216,101,79)
6 organ rgb(221,130,101)
7 mass rgb(144,238,144) Could be tumor or other lesion (M-01000,SRT,"Morphologically Altered Structure") (M-03000,SRT,"Mass") - CID 7159++
8 muscle rgb(192,104,88) (T-D0050,SRT,"Tissue") (T-13001,SRT,"Muscle") - CID 7160 (should refactor)
9 foreign object rgb(220,245,20) Implants, surical instruments, table... (A-00004,SRT,"Physical Object") (M-30400,SRT,"Foreign Body")
10 waste rgb(78,63,0)
11 teeth rgb(255,250,220)
12 fat rgb(230,220,70)
13 gray matter rgb(200,200,235) cf. 39 and 116 (T-D0050,SRT,"Tissue") (T-A0096,SRT,"Gray Matter") - CID 7153 Edited
14 white matter rgb(250,250,210) (T-D0050,SRT,"Tissue") (T-A0095,SRT,"White Matter") - CID 7153 Edited
15 nerve rgb(244,214,49)
16 vein rgb(0,151,206)
17 artery rgb(216,101,79)
18 capillary rgb(183,156,220)
19 ligament rgb(183,214,211)
20 tendon rgb(152,189,207)
21 cartilage rgb(111,184,210)
22 meniscus rgb(178,212,242)
23 lymph node rgb(68,172,100)
24 lymphatic vessel rgb(111,197,131)
25 cerebro-spinal fluid rgb(85,188,255) cf. 106 (T-D0050,SRT,"Tissue") (T-A1000,SRT,"Cerebrospinal Fluid") - CID 7153
26 bile rgb(0,145,30)
27 urine rgb(214,230,130)
28 feces rgb(78,63,0)
29 gas rgb(218,255,255)
30 fluid rgb(170,250,250)
31 edema rgb(140,224,228) (M-01000,SRT,"Morphologically Altered Structure") (M-36300,SRT,"Edema") - CID 7159++
32 bleeding rgb(188,65,28) (M-01000,SRT,"Morphologically Altered Structure") (M-37000,SRT,"Hemorrhage") - CID 7159++
33 necrosis rgb(216,191,216) (M-01000,SRT,"Morphologically Altered Structure") (M-54000,SRT,"Necrosis") - CID 7159
34 clot rgb(145,60,66) (M-01000,SRT,"Morphologically Altered Structure") (M-35000,SRT,"Blood Clot") - CID 7159++
35 embolism rgb(150,98,83) (M-01000,SRT,"Morphologically Altered Structure") (M-35300,SRT,"Embolus") - CID 7159++
36 head rgb(177,122,101)
37 central nervous system rgb(244,214,49)
38 brain rgb(250,250,225) ? tissue or structure (T-A0100,SRT,"Brain") - CID 7153++
39 gray matter of brain rgb(200,200,215) cf. 13 and 116 (T-D0050,SRT,"Tissue") (T-A2020,SRT,"Cerebral Gray Matter") - CID 7153 Edited
40 telencephalon rgb(68,131,98)
41 cerebral cortex rgb(128,174,128)
42 right frontal lobe rgb(83,146,164) (T-D000A,SRT,"Anatomical Structure") (T-A2218,SRT,"Frontal Lobe") - CID 7153++ (G-A100,SRT,"Right")
43 left frontal lobe rgb(83,146,164) (T-D000A,SRT,"Anatomical Structure") (T-A2218,SRT,"Frontal Lobe") - CID 7153++ (G-A101,SRT,"Left")
44 right temporal lobe rgb(162,115,105)
45 left temporal lobe rgb(162,115,105)
46 right parietal lobe rgb(141,93,137)
47 left parietal lobe rgb(141,93,137)
48 right occipital lobe rgb(182,166,110)
49 left occipital lobe rgb(182,166,110)
50 right insular lobe rgb(188,135,166)
51 left insular lobe rgb(188,135,166)
52 right limbic lobe rgb(154,150,201)
53 left limbic lobe rgb(154,150,201)
54 right striatum rgb(177,140,190)
55 left striatum rgb(177,140,190)
56 right caudate nucleus rgb(30,111,85) (T-D000A,SRT,"Anatomical Structure") (T-A3201,SRT,"Caudate Nucleus") - CID 7153++ (G-A100,SRT,"Right")
57 left caudate nucleus rgb(30,111,85) (T-D000A,SRT,"Anatomical Structure") (T-A3201,SRT,"Caudate Nucleus") - CID 7153++ (G-A101,SRT,"Left")
58 right putamen rgb(210,157,166)
59 left putamen rgb(210,157,166)
60 right pallidum rgb(48,129,126)
61 left pallidum rgb(48,129,126)
62 right amygdaloid complex rgb(98,153,112)
63 left amygdaloid complex rgb(98,153,112)
64 diencephalon rgb(69,110,53)
65 thalamus rgb(166,113,137)
66 right thalamus rgb(122,101,38)
67 left thalamus rgb(122,101,38)
68 pineal gland rgb(253,135,192)
69 midbrain rgb(145,92,109)
70 substantia nigra rgb(46,101,131)
71 right substantia nigra rgb(0,108,112)
72 left substantia nigra rgb(0,108,112)
73 cerebral white matter rgb(250,250,225)
74 right superior longitudinal fasciculus rgb(127,150,88) (T-D000A,SRT,"Anatomical Structure") (T-A2820,SRT,"Superior Longitudinal Fasciculus") - CID 7153++ (G-A100,SRT,"Right")
75 left superior longitudinal fasciculus rgb(127,150,88) (T-D000A,SRT,"Anatomical Structure") (T-A2820,SRT,"Superior Longitudinal Fasciculus") - CID 7153++ (G-A101,SRT,"Left")
76 right inferior longitudinal fasciculus rgb(159,116,163)
77 left inferior longitudinal fasciculus rgb(159,116,163)
78 right arcuate fasciculus rgb(125,102,154) DC: SNOMED needs fixing - specifies arcuate as synonym (ratehr than part of) superior longitudinal fasciculus (T-D000A,SRT,"Anatomical Structure") (276650,FMA,"Arcuate Fasciculus") - CID 7153++ (G-A100,SRT,"Right")
79 left arcuate fasciculus rgb(125,102,154) (T-D000A,SRT,"Anatomical Structure") (276650,FMA,"Arcuate Fasciculus") - CID 7153++ (G-A101,SRT,"Left")
80 right uncinate fasciculus rgb(106,174,155) (T-D000A,SRT,"Anatomical Structure") (T-A2831,SRT,"Uncinate Fasciculus") - CID 7153++ (G-A100,SRT,"Right")
81 left uncinate fasciculus rgb(106,174,155) (T-D000A,SRT,"Anatomical Structure") (T-A2831,SRT,"Uncinate Fasciculus") - CID 7153++ (G-A101,SRT,"Left")
82 right cingulum bundle rgb(154,146,83)
83 left cingulum bundle rgb(154,146,83)
84 projection fibers rgb(126,126,55)
85 right corticospinal tract rgb(201,160,133)
86 left corticospinal tract rgb(201,160,133)
87 right optic radiation rgb(78,152,141)
88 left optic radiation rgb(78,152,141)
89 right medial lemniscus rgb(174,140,103)
90 left medial lemniscus rgb(174,140,103)
91 right superior cerebellar peduncle rgb(139,126,177)
92 left superior cerebellar peduncle rgb(139,126,177)
93 right middle cerebellar peduncle rgb(148,120,72)
94 left middle cerebellar peduncle rgb(148,120,72)
95 right inferior cerebellar peduncle rgb(186,135,135)
96 left inferior cerebellar peduncle rgb(186,135,135)
97 optic chiasm rgb(99,106,24)
98 right optic tract rgb(156,171,108)
99 left optic tract rgb(156,171,108)
100 right fornix rgb(64,123,147)
101 left fornix rgb(64,123,147)
102 commissural fibers rgb(138,95,74)
103 corpus callosum rgb(97,113,158)
104 posterior commissure rgb(126,161,197)
105 cerebellar white matter rgb(194,195,164) (T-A6080,SRT,"Cerebellar White Matter") - CID 7153++
106 CSF space rgb(85,188,255) DC: cf. 25; is this one supposed to be brain-specific? assume so (T-A0109,SRT,"Brain Cerebrospinal Fluid Pathway") - CID 7153++
107 ventricles of brain rgb(88,106,215)
108 right lateral ventricle rgb(88,106,215)
109 left lateral ventricle rgb(88,106,215)
110 right third ventricle rgb(88,106,215)
111 left third ventricle rgb(88,106,215)
112 cerebral aqueduct rgb(88,106,215)
113 fourth ventricle rgb(88,106,215)
114 subarachnoid space rgb(88,106,215)
115 spinal cord rgb(244,214,49)
116 gray matter of spinal cord rgb(200,200,215) cf. 7 and 39 (T-A7020,SRT,"Spinal Cord Gray Matter") - CID 7153++
117 white matter of spinal cord rgb(250,250,225) (T-A7070,SRT,"Spinal Cord White Matter") - CID 7153++
118 endocrine system of brain rgb(82,174,128)
119 pituitary gland rgb(57,157,110)
120 adenohypophysis rgb(60,143,83)
121 neurohypophysis rgb(92,162,109)
122 meninges rgb(255,244,209) (T-A1110,SRT,"Meninges") - CID 7153
123 dura mater rgb(255,244,209)
124 arachnoid rgb(255,244,209)
125 pia mater rgb(255,244,209)
126 muscles of head rgb(201,121,77)
127 salivary glands rgb(70,163,117)
128 lips rgb(188,91,95)
129 nose rgb(177,122,101)
130 tongue rgb(166,84,94)
131 soft palate rgb(182,105,107)
132 right inner ear rgb(229,147,118)
133 left inner ear rgb(229,147,118)
134 right external ear rgb(174,122,90)
135 left external ear rgb(174,122,90)
136 right middle ear rgb(201,112,73)
137 left middle ear rgb(201,112,73)
138 right eyeball rgb(194,142,0)
139 left eyeball rgb(194,142,0)
140 skull rgb(241,213,144) (T-11100,SRT,"Skull") - CID 7153
141 right frontal bone rgb(203,179,77)
142 left frontal bone rgb(203,179,77)
143 right parietal bone rgb(229,204,109)
144 left parietal bone rgb(229,204,109)
145 right temporal bone rgb(255,243,152)
146 left temporal bone rgb(255,243,152)
147 right sphenoid bone rgb(209,185,85)
148 left sphenoid bone rgb(209,185,85)
149 right ethmoid bone rgb(248,223,131)
150 left ethmoid bone rgb(248,223,131)
151 occipital bone rgb(255,230,138)
152 maxilla rgb(196,172,68)
153 right zygomatic bone rgb(255,255,167) DC: ? use more general (T-111BE,SRT,"Zygoma"); also, where is the left one ?? (T-11167,SRT,"Zygomatic arch") - CID 4028 (G-A100,SRT,"Right")
154 right lacrimal bone rgb(255,250,160)
155 vomer bone rgb(255,237,145)
156 right palatine bone rgb(242,217,123) (T-111A8,SRT,"Palatine Bone") (G-A100,SRT,"Right")
157 left palatine bone rgb(242,217,123) (T-111A8,SRT,"Palatine Bone") (G-A101,SRT,"Left")
158 mandible rgb(222,198,101)
159 neck rgb(177,122,101)
160 muscles of neck rgb(213,124,109)
161 pharynx rgb(184,105,108)
162 larynx rgb(150,208,243)
163 thyroid gland rgb(62,162,114)
164 right parathyroid glands rgb(62,162,114)
165 left parathyroid glands rgb(62,162,114)
166 skeleton of neck rgb(242,206,142)
167 hyoid bone rgb(250,210,139)
168 cervical vertebral column rgb(255,255,207)
169 thorax rgb(177,122,101)
170 trachea rgb(182,228,255)
171 bronchi rgb(175,216,244) (T-D000A,SRT,"Anatomical Structure") (T-26000,SRT,"Bronchi") - CID 7155
172 right lung rgb(197,165,145) (T-D000A,SRT,"Anatomical Structure") (T-28000,SRT,"Lung") - CID 7155 (G-A100,SRT,"Right")
173 left lung rgb(197,165,145) (T-D000A,SRT,"Anatomical Structure") (T-28000,SRT,"Lung") - CID 7155 (G-A101,SRT,"Left")
174 superior lobe of right lung rgb(172,138,115)
175 superior lobe of left lung rgb(172,138,115)
176 middle lobe of right lung rgb(202,164,140)
177 inferior lobe of right lung rgb(224,186,162)
178 inferior lobe of left lung rgb(224,186,162)
179 pleura rgb(255,245,217)
180 heart rgb(206,110,84) (T-D000A,SRT,"Anatomical Structure") (T-32000,SRT,"Heart") - CID 7152
181 right atrium rgb(210,115,89)
182 left atrium rgb(203,108,81)
183 atrial septum rgb(233,138,112)
184 ventricular septum rgb(195,100,73)
185 right ventricle of heart rgb(181,85,57) DC: SRT code is precordinated; no need for laterality modifier (T-D000A,SRT,"Anatomical Structure") (T-32500,SRT,"Right Ventricle") - CID 7152
186 left ventricle of heart rgb(152,55,13) DC: SRT code is precordinated; no need for laterality modifier (T-D000A,SRT,"Anatomical Structure") (T-32600,SRT,"Left Ventricle") - CID 7152
187 mitral valve rgb(159,63,27)
188 tricuspid valve rgb(166,70,38)
189 aortic valve rgb(218,123,97)
190 pulmonary valve rgb(225,130,104)
191 aorta rgb(224,97,76) DC: ? need specific parts (ascending, arch, descending thoracic, abdominal) (T-D000A,SRT,"Anatomical Structure") (T-42000,SRT,"Aorta") - CID 7152
192 pericardium rgb(255,244,209)
193 pericardial cavity rgb(184,122,154)
194 esophagus rgb(211,171,143)
195 thymus rgb(47,150,103)
196 mediastinum rgb(255,244,209)
197 skin of thoracic wall rgb(173,121,88)
198 muscles of thoracic wall rgb(188,95,76)
199 skeleton of thorax rgb(255,239,172)
200 thoracic vertebral column rgb(226,202,134)
201 ribs rgb(253,232,158)
202 sternum rgb(244,217,154)
203 right clavicle rgb(205,179,108)
204 left clavicle rgb(205,179,108)
205 abdominal cavity rgb(186,124,161)
206 abdomen rgb(177,122,101)
207 peritoneum rgb(255,255,220)
208 omentum rgb(234,234,194)
209 peritoneal cavity rgb(204,142,178)
210 retroperitoneal space rgb(180,119,153)
211 stomach rgb(216,132,105)
212 duodenum rgb(255,253,229)
213 small bowel rgb(205,167,142)
214 colon rgb(204,168,143)
215 anus rgb(255,224,199)
216 liver rgb(221,130,101) (T-D000A,SRT,"Anatomical Structure") (T-62000,SRT,"Liver") - CID 7154
217 biliary tree rgb(0,145,30)
218 gallbladder rgb(139,150,98)
219 pancreas rgb(249,180,111)
220 spleen rgb(157,108,162) (T-D000A,SRT,"Anatomical Structure") (T-C3000,SRT,"Spleen) - CID 7154
221 urinary system rgb(203,136,116)
222 right kidney rgb(185,102,83) (T-D000A,SRT,"Anatomical Structure") (T-71000,SRT,"Kidney") - CID 7154 (G-A100,SRT,"Right")
223 left kidney rgb(185,102,83) (T-D000A,SRT,"Anatomical Structure") (T-71000,SRT,"Kidney") - CID 7154 (G-A101,SRT,"Left")
224 right ureter rgb(247,182,164)
225 left ureter rgb(247,182,164)
226 urinary bladder rgb(222,154,132)
227 urethra rgb(124,186,223)
228 right adrenal gland rgb(249,186,150) (T-D000A,SRT,"Anatomical Structure") (T-B3000,SRT,"Adrenal Gland") (G-A100,SRT,"Right")
229 left adrenal gland rgb(249,186,150) (T-D000A,SRT,"Anatomical Structure") (T-B3000,SRT,"Adrenal Gland") (G-A101,SRT,"Left")
230 female internal genitalia rgb(244,170,147)
231 uterus rgb(255,181,158)
232 right fallopian tube rgb(255,190,165)
233 left fallopian tube rgb(227,153,130)
234 right ovary rgb(213,141,113)
235 left ovary rgb(213,141,113)
236 vagina rgb(193,123,103)
237 male internal genitalia rgb(216,146,127)
238 prostate rgb(230,158,140)
239 right seminal vesicle rgb(245,172,147)
240 left seminal vesicle rgb(245,172,147)
241 right deferent duct rgb(241,172,151)
242 left deferent duct rgb(241,172,151)
243 skin of abdominal wall rgb(177,124,92)
244 muscles of abdominal wall rgb(171,85,68)
245 skeleton of abdomen rgb(217,198,131)
246 lumbar vertebral column rgb(212,188,102)
247 female external genitalia rgb(185,135,134)
248 male external genitalia rgb(185,135,134)
249 skeleton of upper limb rgb(198,175,125)
250 muscles of upper limb rgb(194,98,79)
251 right upper limb rgb(177,122,101)
252 left upper limb rgb(177,122,101)
253 right shoulder rgb(177,122,101)
254 left shoulder rgb(177,122,101)
255 right arm rgb(177,122,101)
256 left arm rgb(177,122,101)
257 right elbow rgb(177,122,101)
258 left elbow rgb(177,122,101)
259 right forearm rgb(177,122,101)
260 left forearm rgb(177,122,101)
261 right wrist rgb(177,122,101)
262 left wrist rgb(177,122,101)
263 right hand rgb(177,122,101)
264 left hand rgb(177,122,101)
265 skeleton of lower limb rgb(255,238,170)
266 muscles of lower limb rgb(206,111,93)
267 right lower limb rgb(177,122,101)
268 left lower limb rgb(177,122,101)
269 right hip rgb(177,122,101)
270 left hip rgb(177,122,101)
271 right thigh rgb(177,122,101)
272 left thigh rgb(177,122,101)
273 right knee rgb(177,122,101)
274 left knee rgb(177,122,101)
275 right leg rgb(177,122,101)
276 left leg rgb(177,122,101)
277 right foot rgb(177,122,101)
278 left foot rgb(177,122,101)
279 peripheral nervous system rgb(216,186,0)
280 autonomic nerve rgb(255,226,77)
281 sympathetic trunk rgb(255,243,106)
282 cranial nerves rgb(255,234,92)
283 vagus nerve rgb(240,210,35)
284 peripheral nerve rgb(224,194,0)
285 circulatory system rgb(213,99,79)
286 systemic arterial system rgb(217,102,81)
287 systemic venous system rgb(0,147,202)
288 pulmonary arterial system rgb(0,122,171)
289 pulmonary venous system rgb(186,77,64)
290 lymphatic system rgb(111,197,131)
291 needle rgb(240,255,30) (A-00004,SRT,"Physical Object") (A-30360,SRT,"Needle") - CID 7157++
292 region 0 rgb(185,232,61)
293 region 1 rgb(0,226,255)
294 region 2 rgb(251,159,255)
295 region 3 rgb(230,169,29)
296 region 4 rgb(0,194,113)
297 region 5 rgb(104,160,249)
298 region 6 rgb(221,108,158)
299 region 7 rgb(137,142,0)
300 region 8 rgb(230,70,0)
301 region 9 rgb(0,147,0)
302 region 10 rgb(0,147,248)
303 region 11 rgb(231,0,206)
304 region 12 rgb(129,78,0)
305 region 13 rgb(0,116,0)
306 region 14 rgb(0,0,255)
307 region 15 rgb(157,0,0)
308 unknown rgb(100,100,130)
309 cyst rgb(205,205,100)

New labels added

integer_label text_label color notes anatomic region anatomic region modifier primary anatomic structure primary anatomic structure modifier segmented property category - CID 7150 segmented property type segmented property type modifier
?? rectum rgba(?,?,?,?) (M-01000,SRT,"Morphologically Altered Structure") (M-3340A,SRT,"Cyst") - CID 7159
?? left testis rgba(?,?,?,?) (T-D000A,SRT,"Anatomical Structure") (T-94000,SRT,"Testis") - CID 7160
?? right testis rgba(?,?,?,?) (T-D000A,SRT,"Anatomical Structure") (T-94000,SRT,"Testis") - CID 7160
?? cervix rgba(?,?,?,?) (T-D000A,SRT,"Anatomical Structure") (T-83200,SRT,"Cervix") - CID 7160
?? diaphragm rgba(?,?,?,?) DC: ? need left/right - probably not (T-D000A,SRT,"Anatomical Structure") (T-D3400,SRT,"Diaphragm) - CID 7155
?? table rgba(?,?,?,?) DC: cf. 9 - table detection is handled specifically by some systems (A-00004,SRT,"Physical Object") (A-17350,SRT,"Table") - CID 7158
?? clothing rgba(?,?,?,?) cf. 9 (A-00004,SRT,"Physical Object") (A-00916,SRT,"Clothing") - CID 7158

Segmentation objects allow to encode recommended display color in "Recommended Display CIELab Value" (0062,000D) attribute; these values are encoded in CIALab.