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))