diff --git a/doc/examples/pm-example-float.json b/doc/examples/pm-example-float.json
index 644dbc6e..c1b8e82c 100644
--- a/doc/examples/pm-example-float.json
+++ b/doc/examples/pm-example-float.json
@@ -28,7 +28,7 @@
},
"SourceImageDiffusionBValues": ["0","1400"],
"AnatomicRegionSequence": {
- "CodeValue": "T-9200B",
+ "CodeValue": "41216001",
"CodingSchemeDesignator": "SCT",
"CodeMeaning": "Prostate"
},
diff --git a/doc/examples/pm-example.json b/doc/examples/pm-example.json
index f313b336..30804721 100644
--- a/doc/examples/pm-example.json
+++ b/doc/examples/pm-example.json
@@ -28,7 +28,7 @@
},
"SourceImageDiffusionBValues": ["0","1400"],
"AnatomicRegionSequence": {
- "CodeValue": "T-9200B",
+ "CodeValue": "41216001",
"CodingSchemeDesignator": "SCT",
"CodeMeaning": "Prostate"
},
diff --git a/doc/segContexts/AnatomicRegionAndModifier-DICOM-Master.json b/doc/segContexts/AnatomicRegionAndModifier-DICOM-Master.json
index 23f018f4..d63bb998 100644
--- a/doc/segContexts/AnatomicRegionAndModifier-DICOM-Master.json
+++ b/doc/segContexts/AnatomicRegionAndModifier-DICOM-Master.json
@@ -202,7 +202,7 @@
"SNOMEDCTConceptID": "7832008"
},
{
- "CodeValue": "T-41070",
+ "CodeValue": "7832008",
"cid": "4030",
"UMLSConceptUID": "C1283352",
"CodeMeaning": "Abdominal aorta and its branches",
@@ -1154,7 +1154,7 @@
"SNOMEDCTConceptID": ""
},
{
- "CodeValue": "T-48052",
+ "CodeValue": "19715009",
"cid": "12108",
"UMLSConceptUID": "",
"CodeMeaning": "Basilic vein",
@@ -2354,7 +2354,7 @@
]
},
{
- "CodeValue": "T-45526",
+ "CodeValue": "11279006",
"cid": "4030",
"UMLSConceptUID": "C1284333",
"CodeMeaning": "Circle of Willis",
@@ -2466,7 +2466,7 @@
"SNOMEDCTConceptID": "71854001"
},
{
- "CodeValue": "D4-31320",
+ "CodeValue": "253276007",
"cid": "3010",
"UMLSConceptUID": "C0018817",
"CodeMeaning": "Common atrium",
@@ -2867,7 +2867,7 @@
"SNOMEDCTConceptID": "25238003"
},
{
- "CodeValue": "T-A0193",
+ "CodeValue": "128320002",
"cid": "4030",
"UMLSConceptUID": "C1280180",
"CodeMeaning": "Cranial venous system",
@@ -3100,7 +3100,7 @@
]
},
{
- "CodeValue": "T-47741",
+ "CodeValue": "86547008",
"cid": "12109",
"UMLSConceptUID": "",
"CodeMeaning": "Dorsalis Pedis Artery",
@@ -3514,7 +3514,7 @@
]
},
{
- "CodeValue": "T-1416B",
+ "CodeValue": "53967007",
"cid": "6116",
"UMLSConceptUID": "C0224353",
"CodeMeaning": "External intercostal muscle",
@@ -5006,7 +5006,7 @@
"SNOMEDCTConceptID": "34516001"
},
{
- "CodeValue": "T-41040",
+ "CodeValue": "299716001",
"cid": "4030",
"UMLSConceptUID": "C1282078",
"CodeMeaning": "Iliac arterial system",
@@ -5100,7 +5100,7 @@
]
},
{
- "CodeValue": "T-48470",
+ "CodeValue": "195416006",
"cid": "3010",
"UMLSConceptUID": "C1267462",
"CodeMeaning": "Inferior cardiac vein",
@@ -5731,7 +5731,7 @@
]
},
{
- "CodeValue": "R-102BC",
+ "CodeValue": "698348000",
"cid": "12105",
"UMLSConceptUID": "",
"CodeMeaning": "Internal Carotid Artery C6 segment",
@@ -5883,7 +5883,7 @@
]
},
{
- "CodeValue": "T-14183",
+ "CodeValue": "41313007",
"cid": "6116",
"UMLSConceptUID": "C0224355",
"CodeMeaning": "Internal intercostal muscle",
@@ -6288,7 +6288,7 @@
"SNOMEDCTConceptID": "4596009"
},
{
- "CodeValue": "T-49423",
+ "CodeValue": "714754004",
"cid": "12110",
"UMLSConceptUID": "",
"CodeMeaning": "Lateral calf perforator",
@@ -6494,7 +6494,7 @@
"SNOMEDCTConceptID": ""
},
{
- "CodeValue": "T-4881F",
+ "CodeValue": "70253006",
"cid": "12114",
"UMLSConceptUID": "",
"CodeMeaning": "Left Main Branch of Portal Vein",
@@ -6530,7 +6530,7 @@
"SNOMEDCTConceptID": "76862008"
},
{
- "CodeValue": "T-43126",
+ "CodeValue": "91760001",
"cid": "3014",
"UMLSConceptUID": "C0278433",
"CodeMeaning": "Left Posterior Descending Artery",
@@ -10027,7 +10027,7 @@
"SNOMEDCTConceptID": ""
},
{
- "CodeValue": "T-4882A",
+ "CodeValue": "73931004",
"cid": "12114",
"UMLSConceptUID": "",
"CodeMeaning": "Right Main Branch of Portal Vein",
@@ -10849,7 +10849,7 @@
]
},
{
- "CodeValue": "T-11500",
+ "CodeValue": "421060004",
"cid": "6114",
"UMLSConceptUID": "C1267072",
"CodeMeaning": "Spine",
@@ -12189,7 +12189,7 @@
]
},
{
- "CodeValue": "T-4942C",
+ "CodeValue": "714759009",
"cid": "12110",
"UMLSConceptUID": "",
"CodeMeaning": "Thigh perforator",
@@ -12514,7 +12514,7 @@
"SNOMEDCTConceptID": ""
},
{
- "CodeValue": "T-141A5",
+ "CodeValue": "88454005",
"cid": "6116",
"UMLSConceptUID": "C0224359",
"CodeMeaning": "Transversus thoracis",
@@ -12740,7 +12740,7 @@
]
},
{
- "CodeValue": "T-48817",
+ "CodeValue": "284639000",
"cid": "12114",
"UMLSConceptUID": "",
"CodeMeaning": "Umbilical Vein",
@@ -12901,7 +12901,7 @@
]
},
{
- "CodeValue": "T-70010",
+ "CodeValue": "431491007",
"cid": "4040",
"UMLSConceptUID": "C0729865",
"CodeMeaning": "Upper urinary tract",
diff --git a/doc/segContexts/SegmentationCategoryTypeModifier-DICOM-Master.json b/doc/segContexts/SegmentationCategoryTypeModifier-DICOM-Master.json
index 41044e68..73412e09 100644
--- a/doc/segContexts/SegmentationCategoryTypeModifier-DICOM-Master.json
+++ b/doc/segContexts/SegmentationCategoryTypeModifier-DICOM-Master.json
@@ -2489,7 +2489,7 @@
"CodingSchemeDesignator": "SCT",
"cid": "6114",
"UMLSConceptUID": "C1267072",
- "CodeValue": "T-11500",
+ "CodeValue": "421060004",
"contextGroupName": "OsseousAnatomyFindingorFeature",
"SNOMEDCTConceptID": "44300000"
},
@@ -3772,7 +3772,7 @@
"CodingSchemeDesignator": "SCT",
"cid": "6116",
"UMLSConceptUID": "C0224353",
- "CodeValue": "T-1416B",
+ "CodeValue": "53967007",
"contextGroupName": "MuscularAnatomy",
"SNOMEDCTConceptID": "244878003"
},
@@ -3859,7 +3859,7 @@
"CodingSchemeDesignator": "SCT",
"cid": "6116",
"UMLSConceptUID": "C0224355",
- "CodeValue": "T-14183",
+ "CodeValue": "41313007",
"contextGroupName": "MuscularAnatomy",
"SNOMEDCTConceptID": "244890001"
},
@@ -3868,7 +3868,7 @@
"CodingSchemeDesignator": "SCT",
"cid": "6116",
"UMLSConceptUID": "C0224359",
- "CodeValue": "T-141A5",
+ "CodeValue": "88454005",
"contextGroupName": "MuscularAnatomy",
"SNOMEDCTConceptID": "244933000"
},
@@ -5934,7 +5934,7 @@
"CodingSchemeDesignator": "SCT",
"cid": "3014",
"UMLSConceptUID": "C0278433",
- "CodeValue": "T-43126",
+ "CodeValue": "91760001",
"contextGroupName": "CoronaryArterySegments",
"SNOMEDCTConceptID": "56322004",
"paired": "N"
@@ -6693,7 +6693,7 @@
"CodingSchemeDesignator": "SCT",
"cid": "4030",
"UMLSConceptUID": "C1284333",
- "CodeValue": "T-45526",
+ "CodeValue": "11279006",
"contextGroupName": "CT,MRandPETAnatomyImaged",
"SNOMEDCTConceptID": "362047009"
},
@@ -8091,7 +8091,7 @@
"CodingSchemeDesignator": "SCT",
"cid": "3010",
"UMLSConceptUID": "C0226661",
- "CodeValue": "T-48440",
+ "CodeValue": "194996006",
"contextGroupName": "CardiovascularAnatomicLocations",
"SNOMEDCTConceptID": "43967001",
"paired": "U"
@@ -8101,7 +8101,7 @@
"CodingSchemeDesignator": "SCT",
"cid": "3010",
"UMLSConceptUID": "C1267462",
- "CodeValue": "T-48470",
+ "CodeValue": "195416006",
"contextGroupName": "CardiovascularAnatomicLocations",
"SNOMEDCTConceptID": "60477001"
},
@@ -8381,7 +8381,7 @@
"CodingSchemeDesignator": "SCT",
"cid": "3010",
"UMLSConceptUID": "C1267489",
- "CodeValue": "T-48817",
+ "CodeValue": "284639000",
"contextGroupName": "CardiovascularAnatomicLocations",
"SNOMEDCTConceptID": "61660003"
},
@@ -8706,7 +8706,7 @@
"CodingSchemeDesignator": "SCT",
"cid": "4",
"UMLSConceptUID": "C0226896",
- "CodeValue": "T-51000",
+ "CodeValue": "123851003",
"contextGroupName": "AnatomicRegion",
"SNOMEDCTConceptID": "21082005",
"paired": "U"
@@ -9759,7 +9759,7 @@
"CodingSchemeDesignator": "SCT",
"cid": "4031",
"UMLSConceptUID": "C1278980",
- "CodeValue": "T-9200B",
+ "CodeValue": "41216001",
"contextGroupName": "CommonAnatomicRegions",
"SNOMEDCTConceptID": "181422007"
},
@@ -10147,7 +10147,7 @@
"CodingSchemeDesignator": "SCT",
"cid": "4030",
"UMLSConceptUID": "C1280180",
- "CodeValue": "T-A0193",
+ "CodeValue": "128320002",
"contextGroupName": "CT,MRandPETAnatomyImaged",
"SNOMEDCTConceptID": "244391007"
},
@@ -12510,7 +12510,7 @@
"CodingSchemeDesignator": "SCT",
"cid": "4",
"UMLSConceptUID": "C0013443",
- "CodeValue": "T-AB000",
+ "CodeValue": "117590005",
"contextGroupName": "AnatomicRegion",
"SNOMEDCTConceptID": "1910005",
"paired": "Y",
diff --git a/doc/segContexts/SegmentationCategoryTypeModifier-SlicerGeneralAnatomy.json b/doc/segContexts/SegmentationCategoryTypeModifier-SlicerGeneralAnatomy.json
index 3de20d2e..e2525bc2 100644
--- a/doc/segContexts/SegmentationCategoryTypeModifier-SlicerGeneralAnatomy.json
+++ b/doc/segContexts/SegmentationCategoryTypeModifier-SlicerGeneralAnatomy.json
@@ -39,7 +39,7 @@
"3dSlicerLabel": "artery",
"cid": "7166",
"UMLSConceptUID": "C0555806",
- "CodeValue": "T-41066",
+ "CodeValue": "51114001",
"contextGroupName": "Common Tissue Segmentation Types",
"SNOMEDCTConceptID": "275989006",
"3dSlicerIntegerLabel": 17
@@ -231,7 +231,7 @@
"3dSlicerLabel": "organ",
"cid": "7166",
"UMLSConceptUID": "C1285092",
- "CodeValue": "T-1A310",
+ "CodeValue": "113343008",
"contextGroupName": "Common Tissue Segmentation Types",
"SNOMEDCTConceptID": "2861001",
"3dSlicerIntegerLabel": 6
@@ -295,7 +295,7 @@
"3dSlicerLabel": "vein",
"cid": "7166",
"UMLSConceptUID": "C0447146",
- "CodeValue": "T-4806E",
+ "CodeValue": "29092000",
"contextGroupName": "Common Tissue Segmentation Types",
"SNOMEDCTConceptID": "181378009",
"3dSlicerIntegerLabel": 16
diff --git a/doc/segContexts/resources/AnatomicRegionAndModifier.xml b/doc/segContexts/resources/AnatomicRegionAndModifier.xml
index ea39b0b4..1de24024 100644
--- a/doc/segContexts/resources/AnatomicRegionAndModifier.xml
+++ b/doc/segContexts/resources/AnatomicRegionAndModifier.xml
@@ -22,7 +22,7 @@
-
+
@@ -141,7 +141,7 @@
-
+
@@ -293,7 +293,7 @@
-
+
@@ -307,7 +307,7 @@
-
+
@@ -357,7 +357,7 @@
-
+
@@ -386,7 +386,7 @@
-
+
@@ -439,7 +439,7 @@
-
+
@@ -632,7 +632,7 @@
-
+
@@ -644,7 +644,7 @@
-
+
@@ -725,7 +725,7 @@
-
+
@@ -745,7 +745,7 @@
-
+
@@ -797,7 +797,7 @@
-
+
@@ -823,11 +823,11 @@
-
+
-
+
@@ -1270,7 +1270,7 @@
-
+
@@ -1373,7 +1373,7 @@
-
+
@@ -1546,7 +1546,7 @@
-
+
@@ -1586,7 +1586,7 @@
-
+
@@ -1615,7 +1615,7 @@
-
+
@@ -1636,7 +1636,7 @@
-
+
diff --git a/doc/segContexts/resources/SegmentationCategoryTypeModifier.json b/doc/segContexts/resources/SegmentationCategoryTypeModifier.json
index 12faec81..b3a730a2 100644
--- a/doc/segContexts/resources/SegmentationCategoryTypeModifier.json
+++ b/doc/segContexts/resources/SegmentationCategoryTypeModifier.json
@@ -49,7 +49,7 @@
"SNOMEDCTConceptID": "91747007"
},
{
- "codeValue": "T-40210",
+ "codeValue": "61695000",
"codingScheme": "SCT",
"UMLSConceptUID": "C0162867",
"cid": "7156",
@@ -112,7 +112,7 @@
"SNOMEDCTConceptID": "85756007"
},
{
- "codeValue": "T-41066",
+ "codeValue": "51114001",
"codingScheme": "SCT",
"UMLSConceptUID": "C0555806",
"cid": "7166",
@@ -247,7 +247,7 @@
"SNOMEDCTConceptID": "119410002"
},
{
- "codeValue": "T-1A310",
+ "codeValue": "113343008",
"codingScheme": "SCT",
"UMLSConceptUID": "C1285092",
"cid": "7166",
@@ -283,7 +283,7 @@
"SNOMEDCTConceptID": "85756007"
},
{
- "codeValue": "T-4806E",
+ "codeValue": "29092000",
"codingScheme": "SCT",
"UMLSConceptUID": "C0447146",
"cid": "7166",
@@ -502,7 +502,7 @@
"SNOMEDCTConceptID": "7832008"
},
{
- "codeValue": "T-41070",
+ "codeValue": "7832008",
"cid": "4030",
"UMLSConceptUID": "C1283352",
"codeMeaning": "Abdominal aorta and its branches",
@@ -1454,7 +1454,7 @@
"SNOMEDCTConceptID": ""
},
{
- "codeValue": "T-48052",
+ "codeValue": "19715009",
"cid": "12108",
"UMLSConceptUID": "",
"codeMeaning": "Basilic vein",
@@ -2654,7 +2654,7 @@
]
},
{
- "codeValue": "T-45526",
+ "codeValue": "11279006",
"cid": "4030",
"UMLSConceptUID": "C1284333",
"codeMeaning": "Circle of Willis",
@@ -2766,7 +2766,7 @@
"SNOMEDCTConceptID": "71854001"
},
{
- "codeValue": "D4-31320",
+ "codeValue": "253276007",
"cid": "3010",
"UMLSConceptUID": "C0018817",
"codeMeaning": "Common atrium",
@@ -3167,7 +3167,7 @@
"SNOMEDCTConceptID": "25238003"
},
{
- "codeValue": "T-A0193",
+ "codeValue": "128320002",
"cid": "4030",
"UMLSConceptUID": "C1280180",
"codeMeaning": "Cranial venous system",
@@ -3400,7 +3400,7 @@
]
},
{
- "codeValue": "T-47741",
+ "codeValue": "86547008",
"cid": "12109",
"UMLSConceptUID": "",
"codeMeaning": "Dorsalis Pedis Artery",
@@ -3814,7 +3814,7 @@
]
},
{
- "codeValue": "T-1416B",
+ "codeValue": "53967007",
"cid": "6116",
"UMLSConceptUID": "C0224353",
"codeMeaning": "External intercostal muscle",
@@ -5306,7 +5306,7 @@
"SNOMEDCTConceptID": "34516001"
},
{
- "codeValue": "T-41040",
+ "codeValue": "299716001",
"cid": "4030",
"UMLSConceptUID": "C1282078",
"codeMeaning": "Iliac arterial system",
@@ -5400,7 +5400,7 @@
]
},
{
- "codeValue": "T-48470",
+ "codeValue": "195416006",
"cid": "3010",
"UMLSConceptUID": "C1267462",
"codeMeaning": "Inferior cardiac vein",
@@ -6031,7 +6031,7 @@
]
},
{
- "codeValue": "R-102BC",
+ "codeValue": "698348000",
"cid": "12105",
"UMLSConceptUID": "",
"codeMeaning": "Internal Carotid Artery C6 segment",
@@ -6183,7 +6183,7 @@
]
},
{
- "codeValue": "T-14183",
+ "codeValue": "41313007",
"cid": "6116",
"UMLSConceptUID": "C0224355",
"codeMeaning": "Internal intercostal muscle",
@@ -6588,7 +6588,7 @@
"SNOMEDCTConceptID": "4596009"
},
{
- "codeValue": "T-49423",
+ "codeValue": "714754004",
"cid": "12110",
"UMLSConceptUID": "",
"codeMeaning": "Lateral calf perforator",
@@ -6794,7 +6794,7 @@
"SNOMEDCTConceptID": ""
},
{
- "codeValue": "T-4881F",
+ "codeValue": "70253006",
"cid": "12114",
"UMLSConceptUID": "",
"codeMeaning": "Left Main Branch of Portal Vein",
@@ -6830,7 +6830,7 @@
"SNOMEDCTConceptID": "76862008"
},
{
- "codeValue": "T-43126",
+ "codeValue": "91760001",
"cid": "3014",
"UMLSConceptUID": "C0278433",
"codeMeaning": "Left Posterior Descending Artery",
@@ -10327,7 +10327,7 @@
"SNOMEDCTConceptID": ""
},
{
- "codeValue": "T-4882A",
+ "codeValue": "73931004",
"cid": "12114",
"UMLSConceptUID": "",
"codeMeaning": "Right Main Branch of Portal Vein",
@@ -11149,7 +11149,7 @@
]
},
{
- "codeValue": "T-11500",
+ "codeValue": "421060004",
"cid": "6114",
"UMLSConceptUID": "C1267072",
"codeMeaning": "Spine",
@@ -12489,7 +12489,7 @@
]
},
{
- "codeValue": "T-4942C",
+ "codeValue": "714759009",
"cid": "12110",
"UMLSConceptUID": "",
"codeMeaning": "Thigh perforator",
@@ -12814,7 +12814,7 @@
"SNOMEDCTConceptID": ""
},
{
- "codeValue": "T-141A5",
+ "codeValue": "88454005",
"cid": "6116",
"UMLSConceptUID": "C0224359",
"codeMeaning": "Transversus thoracis",
@@ -13040,7 +13040,7 @@
]
},
{
- "codeValue": "T-48817",
+ "codeValue": "284639000",
"cid": "12114",
"UMLSConceptUID": "",
"codeMeaning": "Umbilical Vein",
@@ -13201,7 +13201,7 @@
]
},
{
- "codeValue": "T-70010",
+ "codeValue": "431491007",
"cid": "4040",
"UMLSConceptUID": "C0729865",
"codeMeaning": "Upper urinary tract",
@@ -13716,7 +13716,7 @@
},
{
"codeValue": "A-26A06",
- "codingScheme": "SCT",
+ "codingScheme": "SRT",
"UMLSConceptUID": "",
"cid": "8",
"contextGroupName": "Angiographic Interventional Devices",
@@ -13725,7 +13725,7 @@
},
{
"codeValue": "A-26A08",
- "codingScheme": "SCT",
+ "codingScheme": "SRT",
"UMLSConceptUID": "",
"cid": "8",
"contextGroupName": "Angiographic Interventional Devices",
@@ -13913,7 +13913,7 @@
"SNOMEDCTConceptID": "56353002"
},
{
- "codeValue": "A-13510",
+ "codeValue": "27065002",
"codingScheme": "SCT",
"UMLSConceptUID": "C0038969",
"cid": "6040",
@@ -14138,7 +14138,7 @@
"SNOMEDCTConceptID": "56353002"
},
{
- "codeValue": "A-13510",
+ "codeValue": "27065002",
"codingScheme": "SCT",
"UMLSConceptUID": "C0038969",
"cid": "6138",
diff --git a/doc/segContexts/resources/SegmentationCategoryTypeModifier.xml b/doc/segContexts/resources/SegmentationCategoryTypeModifier.xml
index 990a51c3..ea7a1f27 100644
--- a/doc/segContexts/resources/SegmentationCategoryTypeModifier.xml
+++ b/doc/segContexts/resources/SegmentationCategoryTypeModifier.xml
@@ -5,14 +5,14 @@
-
+
-
+
@@ -27,11 +27,11 @@
-
+
-
+
@@ -56,7 +56,7 @@
-
+
@@ -175,7 +175,7 @@
-
+
@@ -327,7 +327,7 @@
-
+
@@ -341,7 +341,7 @@
-
+
@@ -391,7 +391,7 @@
-
+
@@ -420,7 +420,7 @@
-
+
@@ -473,7 +473,7 @@
-
+
@@ -666,7 +666,7 @@
-
+
@@ -678,7 +678,7 @@
-
+
@@ -759,7 +759,7 @@
-
+
@@ -779,7 +779,7 @@
-
+
@@ -831,7 +831,7 @@
-
+
@@ -857,11 +857,11 @@
-
+
-
+
@@ -1304,7 +1304,7 @@
-
+
@@ -1407,7 +1407,7 @@
-
+
@@ -1580,7 +1580,7 @@
-
+
@@ -1620,7 +1620,7 @@
-
+
@@ -1649,7 +1649,7 @@
-
+
@@ -1670,7 +1670,7 @@
-
+
@@ -1734,8 +1734,8 @@
-
-
+
+
@@ -1756,7 +1756,7 @@
-
+
@@ -1781,7 +1781,7 @@
-
+
diff --git a/doc/segContexts/resources/SlicerGenericAnatomy.csv b/doc/segContexts/resources/SlicerGenericAnatomy.csv
index e1c4afdc..f5bd83d0 100644
--- a/doc/segContexts/resources/SlicerGenericAnatomy.csv
+++ b/doc/segContexts/resources/SlicerGenericAnatomy.csv
@@ -5,7 +5,7 @@ Integer Label,Text Label,Anatomic Region,Anatomic Region Modifier,Primary Anatom
3, skin , , , , ," (85756007,SCT,""Tissue"") ","(39937001,SCT,""Skin"")",716y, ," rgb(177,122,101) ", ,
4, connective tissue , , , , ," (85756007,SCT,""Tissue"") ","(21793004,SCT,""Connective tissue"")",716y, ," rgb(111,184,210) ", ,
5, blood , , , , ,"(91720002,SCT,""Body Substance"")","(87612001,SCT,""Blood"")",716y, ," rgb(216,101,79) ", ,
-6, organ , , , , ," (85756007,SCT,""Tissue"") ","(T-1A310,SCT,""Organ"")",716y, ," rgb(221,130,101) ", ,
+6, organ , , , , ," (85756007,SCT,""Tissue"") ","(113343008,SCT,""Organ"")",716y, ," rgb(221,130,101) ", ,
7, mass , , , , ," (49755003,SCT,""Morphologically Altered Structure"") ","(4147007,SCT,""Mass"")",7159++, ," rgb(144,238,144) ", Could be tumor or other lesion ,
8, muscle , , , , ," (85756007,SCT,""Tissue"") ","(71616004,SCT,""Muscle"")",716y, ," rgb(192,104,88) ", ,
9, foreign object , , , , ," (260787004,SCT,""Physical Object"") ","(19227008,SCT,""Foreign body"") ",7158++, ," rgb(220,245,20) "," Implants, surical instruments, table... ",
@@ -15,8 +15,8 @@ Integer Label,Text Label,Anatomic Region,Anatomic Region Modifier,Primary Anatom
13, gray matter , , , , ," (85756007,SCT,""Tissue"") ","(389081007,SCT,""Gray matter"")",7153 edited, ," rgb(200,200,235) ", cf. #39 #116 ,
14, white matter , , , , ," (85756007,SCT,""Tissue"") ","(389080008,SCT,""White matter"")",7153 edited, ," rgb(250,250,210) ", ,
15, nerve , , , , ," (85756007,SCT,""Tissue"") ","(119410002,SCT,""Nerve"")",716y, ," rgb(244,214,49) ", ,
-16, vein , , , , ," (85756007,SCT,""Tissue"") ","(T-4806E,SCT,""Vein"")",716y, ," rgb(0,151,206) ", ,
-17, artery , , , , ," (85756007,SCT,""Tissue"") ","(T-41066,SCT,""Artery"")",716y, ," rgb(216,101,79) ", ,
+16, vein , , , , ," (85756007,SCT,""Tissue"") ","(29092000,SCT,""Vein"")",716y, ," rgb(0,151,206) ", ,
+17, artery , , , , ," (85756007,SCT,""Tissue"") ","(51114001,SCT,""Artery"")",716y, ," rgb(216,101,79) ", ,
18, capillary , , , , ," (85756007,SCT,""Tissue"") ","(20982000,SCT,""Capillary"")",716y, ," rgb(183,156,220) ", ,
19, ligament , , , , ," (85756007,SCT,""Tissue"") ","(52082005,SCT,""Ligament"")",716y, ," rgb(183,214,211) ", ,
20, tendon , , , , ," (85756007,SCT,""Tissue"") ","(13024002,SCT,""Tendon"")",716y, ," rgb(152,189,207) ", ,
@@ -154,11 +154,11 @@ Integer Label,Text Label,Anatomic Region,Anatomic Region Modifier,Primary Anatom
150, left ethmoid bone , , , , ," (123037004,SCT,""Anatomical Structure"") "," (52374004,SCT,""Ethmoid bone"")",4028++," (7771000,SCT,""Left"") "," rgb(248,223,131) ", ,
151, occipital bone , , , , ," (123037004,SCT,""Anatomical Structure"") "," (31640002,SCT,""Occipital bone"")",4028++, ," rgb(255,230,138) ", ,
152, maxilla , , , , ," (123037004,SCT,""Anatomical Structure"") "," (70925003,SCT,""Maxilla"")",4028, ," rgb(196,172,68) ", ,
-153, right zygomatic bone ,"(T-11167,SCT,""Zygomatic arch"")"," (24028007,SCT,""Right"") ", , ," (123037004,SCT,""Anatomical Structure"") ","(13881006,SCT,""Zygoma"")",4028++," (24028007,SCT,""Right"") "," rgb(255,255,167) ","? use more general (T-111BE,SCT,""Zygoma""), also, where is the left one ?? ",
+153, right zygomatic bone ,"(13881006,SCT,""Zygomatic arch"")"," (24028007,SCT,""Right"") ", , ," (123037004,SCT,""Anatomical Structure"") ","(13881006,SCT,""Zygoma"")",4028++," (24028007,SCT,""Right"") "," rgb(255,255,167) ","? use more general (13881006,SCT,""Zygoma""), also, where is the left one ?? ",
154, right lacrimal bone , , , , ," (123037004,SCT,""Anatomical Structure"") "," (6229007,SCT,""Lacrimal bone"") ",4028++," (24028007,SCT,""Right"") "," rgb(255,250,160) ",where is the left one ?? ,
155, vomer bone , , , , ," (123037004,SCT,""Anatomical Structure"") "," (87166008,SCT,""Vomer bone"")",4028++, ," rgb(255,237,145) ", ,
-156, right palatine bone ," (T-111A8,SCT,""Palatine Bone"") "," (24028007,SCT,""Right"") ", , ," (123037004,SCT,""Anatomical Structure"") "," (51283005,SCT,""Palatine bone"") ",4028++," (24028007,SCT,""Right"") "," rgb(242,217,123) ", ,
-157, left palatine bone ," (T-111A8,SCT,""Palatine Bone"") "," (7771000,SCT,""Left"") ", , ," (123037004,SCT,""Anatomical Structure"") "," (51283005,SCT,""Palatine bone"") ",4028++," (7771000,SCT,""Left"") "," rgb(242,217,123) ", ,
+156, right palatine bone ," (51283005,SCT,""Palatine Bone"") "," (24028007,SCT,""Right"") ", , ," (123037004,SCT,""Anatomical Structure"") "," (51283005,SCT,""Palatine bone"") ",4028++," (24028007,SCT,""Right"") "," rgb(242,217,123) ", ,
+157, left palatine bone ," (51283005,SCT,""Palatine Bone"") "," (7771000,SCT,""Left"") ", , ," (123037004,SCT,""Anatomical Structure"") "," (51283005,SCT,""Palatine bone"") ",4028++," (7771000,SCT,""Left"") "," rgb(242,217,123) ", ,
158, mandible , , , , ," (123037004,SCT,""Anatomical Structure"") "," (91609006,SCT,""Mandible"")",4028, ," rgb(222,198,101) ", ,
159, neck , , , , ," (123037004,SCT,""Anatomical Structure"") "," (45048000,SCT,""Neck"")",4028, ," rgb(177,122,101) ", ,
160, muscles of neck , , , , ," (123037004,SCT,""Anatomical Structure"") ","(81727001,SCT,""Muscle of neck"") ",4028++, ," rgb(213,124,109) ", ,
@@ -258,8 +258,8 @@ Integer Label,Text Label,Anatomic Region,Anatomic Region Modifier,Primary Anatom
254, left shoulder , , , , ," (123037004,SCT,""Anatomical Structure"") "," (16982005,SCT,""Shoulder"")",4031," (7771000,SCT,""Left"") "," rgb(177,122,101) ","Code is region, not joint",
255, right arm , , , , ," (123037004,SCT,""Anatomical Structure"") "," (40983000,SCT,""Upper arm"")",4031," (24028007,SCT,""Right"") "," rgb(177,122,101) ", ,
256, left arm , , , , ," (123037004,SCT,""Anatomical Structure"") "," (40983000,SCT,""Upper arm"")",4031," (7771000,SCT,""Left"") "," rgb(177,122,101) ", ,
-257, right elbow , , , , ," (123037004,SCT,""Anatomical Structure"") "," (T-D0678,SCT,""Elbow"")",4031," (24028007,SCT,""Right"") "," rgb(177,122,101) ","Code is region, not joint",
-258, left elbow , , , , ," (123037004,SCT,""Anatomical Structure"") "," (T-D0678,SCT,""Elbow"")",4031," (7771000,SCT,""Left"") "," rgb(177,122,101) ","Code is region, not joint",
+257, right elbow , , , , ," (123037004,SCT,""Anatomical Structure"") "," (16953009,SCT,""Elbow"")",4031," (24028007,SCT,""Right"") "," rgb(177,122,101) ","Code is region, not joint",
+258, left elbow , , , , ," (123037004,SCT,""Anatomical Structure"") "," (16953009,SCT,""Elbow"")",4031," (7771000,SCT,""Left"") "," rgb(177,122,101) ","Code is region, not joint",
259, right forearm , , , , ," (123037004,SCT,""Anatomical Structure"") "," (14975008,SCT,""Forearm"")",4031," (24028007,SCT,""Right"") "," rgb(177,122,101) ", ,
260, left forearm , , , , ," (123037004,SCT,""Anatomical Structure"") "," (14975008,SCT,""Forearm"")",4031," (7771000,SCT,""Left"") "," rgb(177,122,101) ", ,
261, right wrist , , , , ," (123037004,SCT,""Anatomical Structure"") "," (8205005,SCT,""Wrist"")",4031," (24028007,SCT,""Right"") "," rgb(177,122,101) ","Code is region, not joint",
diff --git a/util/measurementReportUtils/codeSequences.py b/util/measurementReportUtils/codeSequences.py
index c999ba34..48d2b6ae 100644
--- a/util/measurementReportUtils/codeSequences.py
+++ b/util/measurementReportUtils/codeSequences.py
@@ -17,7 +17,7 @@ def __init__(self, segmentedStructure):
elif segmentedStructure == "TumorROI_PZ_1":
super().__init__("Abnormal", "SCT", "263654008")
elif segmentedStructure == "WholeGland":
- super().__init__("Entire Gland", "SCT", "T-F6078")
+ super().__init__("Entire Gland", "SCT", "714645007")
else:
raise ValueError("Segmented Structure Type {} is not supported yet. Build your own Finding code sequence using the class CodeSequence".format(segmentedStructure))
@@ -26,13 +26,13 @@ class FindingSite(CodeSequence):
def __init__(self, segmentedStructure):
if segmentedStructure == "NormalROI_PZ_1":
- super().__init__("Peripheral zone of the prostate", "SCT", "T-D05E4")
+ super().__init__("Peripheral zone of the prostate", "SCT", "279706003")
elif segmentedStructure == "PeripheralZone":
- super().__init__("Peripheral zone of the prostate", "SCT", "T-D05E4")
+ super().__init__("Peripheral zone of the prostate", "SCT", "279706003")
elif segmentedStructure == "TumorROI_PZ_1":
- super().__init__("Peripheral zone of the prostate", "SCT", "T-D05E4")
+ super().__init__("Peripheral zone of the prostate", "SCT", "279706003")
elif segmentedStructure == "WholeGland":
- super().__init__("Prostate", "SCT", "T-9200B")
+ super().__init__("Prostate", "SCT", "41216001")
else:
raise ValueError("Segmented Structure Type {} is not supported yet. Build your own FindingSite code sequence using the class CodeSequence".format(segmentedStructure))