diff --git a/Dockerfile b/Dockerfile
index f13fff01bd1405023b5479bf74c9d55dde5774f6..62d83bb2de3faa969d4d4f86c782517cb6bbce9e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -7,7 +7,7 @@ ARG USE_LOGO
ENV USE_LOGO=${USE_LOGO:-hbp}
ARG DATASET_PREVIEW_URL
-ENV DATASET_PREVIEW_URL=${DATASET_PREVIEW_URL:-https://hbp-kg-dataset-previewer.apps.hbp.eu/datasetPreview}
+ENV DATASET_PREVIEW_URL=${DATASET_PREVIEW_URL:-https://hbp-kg-dataset-previewer.apps.hbp.eu/v2}
ARG USE_LOGO
ENV USE_LOGO=${USE_LOGO:-hbp}
diff --git a/deploy/datasets/util.js b/deploy/datasets/util.js
index 25953080f60a025c8d321ee976dd50cf894cc4f3..d59ddd5f17d9bbaf1e89a88ba7b012c2e89b1cdd 100644
--- a/deploy/datasets/util.js
+++ b/deploy/datasets/util.js
@@ -97,7 +97,7 @@ initPrArray.push(
.then(json => {
const longBundle = flattenRegions(json.parcellations.find(({ name }) => name === 'Fibre Bundle Atlas - Long Bundle').regions)
const shortBundle = flattenRegions(json.parcellations.find(({ name }) => name === 'Fibre Bundle Atlas - Short Bundle').regions)
- const jubrain = flattenRegions(json.parcellations.find(({ name }) => 'JuBrain Cytoarchitectonic Atlas' === name).regions)
+ const jubrain = flattenRegions(json.parcellations.find(({ name }) => 'Cytoarchitectonic Maps' === name).regions)
longBundleSet = populateSet(longBundle)
shortBundleSet = populateSet(shortBundle)
juBrainSet = populateSet(jubrain)
diff --git a/docs/releases/v2.2.6.md b/docs/releases/v2.2.6.md
index dcf0d026c6f8ce7ec08c53922837ce5d715bbb98..717faaf5a20dab8896bfaea6da9e9d4ca6577969 100644
--- a/docs/releases/v2.2.6.md
+++ b/docs/releases/v2.2.6.md
@@ -1,5 +1,9 @@
# v2.2.6
+## Feat
+
+- Added Julich Brain v2.4 to the supported atlases
+
## Bugfixes
- Fixed matomo CSP issues
diff --git a/src/res/ext/MNI152.json b/src/res/ext/MNI152.json
index 62aa2e7212dbc857050080e32fe663fc2f63ef4a..2ee0837e020edf79c720065ef0504b8236807319 100644
--- a/src/res/ext/MNI152.json
+++ b/src/res/ext/MNI152.json
@@ -8,13 +8,15 @@
"nehubaConfigURL": "nehubaConfig/MNI152NehubaConfig",
"otherNgIds": [
"jubrain mni152 v18 left",
- "jubrain mni152 v18 right"
+ "jubrain mni152 v18 right",
+ "julich brain mni152 v22 left",
+ "julich brain mni152 v22 right"
],
"parcellations": [
{
- "name": "JuBrain Cytoarchitectonic Atlas",
- "displayName":"Julich-Brain Cytoarchitectonic Atlas",
- "ngId": "julich brain mni152 v22 left",
+ "fullId": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+ "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+ "name": "Cytoarchitectonic Maps",
"auxillaryMeshIndices": [
65535
],
@@ -24,12 +26,11 @@
"originDatasets": [
{
"kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "fd303d56-e1aa-46a2-9d0c-7e5215aeb7ca"
+ "kgId": "4ac9f0bc-560d-47e0-8916-7b24da9bb0ce"
}
],
"properties": {
- "version": "1.0",
- "description": "This dataset contains the whole-brain parcellation of the JuBrain Cytoarchitectonic Atlas (Amunts and Zilles, 2015) in the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. The parcellation is derived from the individual probability maps (PMs) of the cytoarchitectonic regions released in the JuBrain Atlas, that are further combined into a Maximum Probability Map (MPM). The MPM is calculated by considering for each voxel the probability of all cytoarchitectonic areas released in the atlas, and determining the most probable assignment (Eickhoff 2005). Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets.",
+ "description": "This dataset contains the whole-brain parcellation of the JuBrain Cytoarchitectonic Atlas (Amunts and Zilles, 2015) in the MNI ICBM 2009c Asymmetric as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. The parcellation is derived from the individual probability maps (PMs) of the cytoarchitectonic regions released in the JuBrain Atlas, that are further combined into a Maximum Probability Map (MPM). The MPM is calculated by considering for each voxel the probability of all cytoarchitectonic areas released in the atlas, and determining the most probable assignment (Eickhoff 2005). Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets.",
"publications": [
{
"doi": "https://doi.org/10.1038/nrn2776",
@@ -45,10246 +46,12505 @@
}
]
},
- "_meta": {
- "regions": {
- "repo": "https://gin.g-node.org/xgui3783/20200811-julich-brain-v2-ontology.git",
- "commit": "c6d48db10fff65def20f39aa2ef1d6e4454b1b4c"
- }
- },
"regions": [
{
"name": "telencephalon",
"status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
"children": [
{
"name": "cerebral nuclei",
"status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
"children": [
{
"name": "basal forebrain",
"status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
"children": [
{
"name": "magnocellular group within septum",
"status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
"children": [
{
"name": "Ch 123 (Basal Forebrain)",
- "arealabel": "Ch-123",
"status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/7SEP-P2V",
- "synonyms": [],
- "rgb": null,
"children": [
{
"name": "Ch 123 (Basal Forebrain)",
- "arealabel": "Ch-123",
"status": "left hemisphere",
- "labelIndex": 75,
- "doi": "https://doi.org/10.25493/7SEP-P2V",
- "synonyms": [],
- "rgb": null,
- "children": [],
+ "labelIndex": 76,
+ "rgb": [
+ 200,
+ 200,
+ 200
+ ],
+ "ngId": "ICBM152_V24_LEFT_NG",
+ "originDatasets": [
+ {
+ "filename": "Ch 123 (Basal Forebrain) [v4.2, ICBM 2009c Asymmetric, left hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "147aaab9-d5f2-48db-80f3-95adc9e7e8a6"
+ }
+ ],
"fullId": {
"kg": {
"kgSchema": "minds/core/parcellationregion/v1.0.0",
"kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
}
},
- "relatedAreas": [],
- "ngId": "julich brain mni152 v22 left",
- "originDatasets": [
- {
- "kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "147aaab9-d5f2-48db-80f3-95adc9e7e8a6",
- "filename": "Ch 123 (Basal Forebrain) [v4.2, ICBM 2009c Asymmetric, left hemisphere]"
+ "_": {
+ "xml": {
+ "name": "Ch 123 (Basal Forebrain)",
+ "id": "286",
+ "grayvalue": "76"
+ },
+ "dat": {
+ "colors": false,
+ "names": false
}
- ],
- "ontologyLabelIndex": 286
+ }
},
{
"name": "Ch 123 (Basal Forebrain)",
- "arealabel": "Ch-123",
"status": "right hemisphere",
"labelIndex": 76,
- "doi": "https://doi.org/10.25493/7SEP-P2V",
- "synonyms": [],
- "rgb": null,
- "children": [],
+ "rgb": [
+ 200,
+ 200,
+ 200
+ ],
+ "ngId": "ICBM152_V24_RIGHT_NG",
+ "originDatasets": [
+ {
+ "filename": "Ch 123 (Basal Forebrain) [v4.2, ICBM 2009c Asymmetric, right hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "147aaab9-d5f2-48db-80f3-95adc9e7e8a6"
+ }
+ ],
"fullId": {
"kg": {
"kgSchema": "minds/core/parcellationregion/v1.0.0",
"kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
}
},
- "relatedAreas": [],
- "ngId": "julich brain mni152 v22 right",
- "originDatasets": [
- {
- "kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "147aaab9-d5f2-48db-80f3-95adc9e7e8a6",
- "filename": "Ch 123 (Basal Forebrain) [v4.2, ICBM 2009c Asymmetric, right hemisphere]"
+ "_": {
+ "xml": {
+ "name": "Ch 123 (Basal Forebrain)",
+ "id": "286",
+ "grayvalue": "76"
+ },
+ "dat": {
+ "colors": false,
+ "names": false
}
- ],
- "ontologyLabelIndex": 286
+ }
}
],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
+ "_": {
+ "jubrain-ontology_24.json": {
+ "name": "Ch 123 (Basal Forebrain)",
+ "arealabel": "Ch-123",
+ "status": "publicP",
+ "labelIndex": "286",
+ "doi": "https://doi.org/10.25493/7SEP-P2V",
+ "synonyms": [],
+ "rgb": null,
+ "kgHref": "https://kg.ebrains.eu/instances/Dataset/147aaab9-d5f2-48db-80f3-95adc9e7e8a6"
+ },
+ "kgRegion": {
+ "alternateOf": [],
+ "species": [],
+ "name": "Ch 123 (Basal Forebrain)",
+ "alias": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/bb111a95-e04c-4987-8254-4af4ed8b0022"
}
- },
- "relatedAreas": []
+ }
}
- ]
+ ],
+ "_": {
+ "jubrain-ontology_24.json": {
+ "name": "magnocellular group within septum",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
+ }
+ }
},
{
"name": "sublenticular part of basal forebrain",
"status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
"children": [
{
"name": "Ch 4 (Basal Forebrain)",
- "arealabel": "Ch-4",
"status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/VZJ5-8WJ",
- "synonyms": [],
- "rgb": null,
"children": [
{
"name": "Ch 4 (Basal Forebrain)",
- "arealabel": "Ch-4",
"status": "left hemisphere",
"labelIndex": 12,
- "doi": "https://doi.org/10.25493/VZJ5-8WJ",
- "synonyms": [],
- "rgb": null,
- "children": [],
+ "rgb": [
+ 200,
+ 200,
+ 200
+ ],
+ "ngId": "ICBM152_V24_LEFT_NG",
+ "originDatasets": [
+ {
+ "filename": "Ch 4 (Basal Forebrain) [v4.2, ICBM 2009c Asymmetric, left hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "791a14c8-b899-414f-b237-27574a4cce7e"
+ }
+ ],
"fullId": {
"kg": {
"kgSchema": "minds/core/parcellationregion/v1.0.0",
"kgId": "a5c9d95f-8e7c-4454-91b6-a790387370fc"
}
},
- "relatedAreas": [],
- "ngId": "julich brain mni152 v22 left",
- "originDatasets": [
- {
- "kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "791a14c8-b899-414f-b237-27574a4cce7e",
- "filename": "Ch 4 (Basal Forebrain) [v4.2, ICBM 2009c Asymmetric, left hemisphere]"
+ "_": {
+ "xml": {
+ "name": "Ch 4 (Basal Forebrain)",
+ "id": "264",
+ "grayvalue": "12"
+ },
+ "dat": {
+ "colors": false,
+ "names": false
}
- ],
- "ontologyLabelIndex": 264
+ }
},
{
"name": "Ch 4 (Basal Forebrain)",
- "arealabel": "Ch-4",
"status": "right hemisphere",
"labelIndex": 12,
- "doi": "https://doi.org/10.25493/VZJ5-8WJ",
- "synonyms": [],
- "rgb": null,
- "children": [],
+ "rgb": [
+ 200,
+ 200,
+ 200
+ ],
+ "ngId": "ICBM152_V24_RIGHT_NG",
+ "originDatasets": [
+ {
+ "filename": "Ch 4 (Basal Forebrain) [v4.2, ICBM 2009c Asymmetric, right hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "791a14c8-b899-414f-b237-27574a4cce7e"
+ }
+ ],
"fullId": {
"kg": {
"kgSchema": "minds/core/parcellationregion/v1.0.0",
"kgId": "a5c9d95f-8e7c-4454-91b6-a790387370fc"
}
},
- "relatedAreas": [],
- "ngId": "julich brain mni152 v22 right",
- "originDatasets": [
- {
- "kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "791a14c8-b899-414f-b237-27574a4cce7e",
- "filename": "Ch 4 (Basal Forebrain) [v4.2, ICBM 2009c Asymmetric, right hemisphere]"
+ "_": {
+ "xml": {
+ "name": "Ch 4 (Basal Forebrain)",
+ "id": "264",
+ "grayvalue": "12"
+ },
+ "dat": {
+ "colors": false,
+ "names": false
}
- ],
- "ontologyLabelIndex": 264
+ }
}
],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "a5c9d95f-8e7c-4454-91b6-a790387370fc"
+ "_": {
+ "jubrain-ontology_24.json": {
+ "name": "Ch 4 (Basal Forebrain)",
+ "arealabel": "Ch-4",
+ "status": "publicP",
+ "labelIndex": "264",
+ "doi": "https://doi.org/10.25493/VZJ5-8WJ",
+ "synonyms": [],
+ "rgb": null,
+ "kgHref": "https://kg.ebrains.eu/search/instances/Dataset/791a14c8-b899-414f-b237-27574a4cce7e"
+ },
+ "kgRegion": {
+ "alternateOf": [],
+ "species": [],
+ "name": "Ch 4 (Basal Forebrain)",
+ "alias": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/a5c9d95f-8e7c-4454-91b6-a790387370fc"
}
- },
- "relatedAreas": []
+ }
+ }
+ ],
+ "_": {
+ "jubrain-ontology_24.json": {
+ "name": "sublenticular part of basal forebrain",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
}
- ]
+ }
},
{
"name": "magnocellular group within horizontal limb of diagnoal band",
"status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
"children": [
{
"name": "Ch 123 (Basal Forebrain)",
- "arealabel": "Ch-123",
"status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/7SEP-P2V",
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "Ch 123 (Basal Forebrain)",
- "arealabel": "Ch-123",
- "status": "left hemisphere",
- "labelIndex": "286",
- "doi": "https://doi.org/10.25493/7SEP-P2V",
- "synonyms": [],
- "rgb": null,
- "children": [],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
- }
- },
- "relatedAreas": [],
- "ngId": "julich brain mni152 v22 left",
- "originDatasets": [
- {
- "kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "147aaab9-d5f2-48db-80f3-95adc9e7e8a6",
- "filename": "Ch 123 (Basal Forebrain) [v4.2, ICBM 2009c Asymmetric, left hemisphere]"
- }
- ]
- },
- {
+ "children": [],
+ "_": {
+ "jubrain-ontology_24.json": {
"name": "Ch 123 (Basal Forebrain)",
"arealabel": "Ch-123",
- "status": "right hemisphere",
+ "status": "publicP",
"labelIndex": "286",
"doi": "https://doi.org/10.25493/7SEP-P2V",
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- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
+ "kgHref": "https://kg.ebrains.eu/instances/Dataset/147aaab9-d5f2-48db-80f3-95adc9e7e8a6"
}
- },
- "relatedAreas": []
+ }
+ }
+ ],
+ "_": {
+ "jubrain-ontology_24.json": {
+ "name": "magnocellular group within horizontal limb of diagnoal band",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
}
- ]
+ }
+ }
+ ],
+ "_": {
+ "jubrain-ontology_24.json": {
+ "name": "basal forebrain",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
}
- ]
+ }
},
{
"name": "amygdala",
"status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
"children": [
{
"name": "laterobasal group",
"status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
"children": [
{
"name": "LB (Amygdala)",
- "arealabel": "LB",
"status": "publicP",
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- "synonyms": [],
- "rgb": null,
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- "labelIndex": 90,
- "doi": "https://doi.org/10.25493/C3X0-NV3",
- "synonyms": [],
- "rgb": null,
- "children": [],
+ "labelIndex": 91,
+ "rgb": [
+ 200,
+ 200,
+ 200
+ ],
+ "ngId": "ICBM152_V24_LEFT_NG",
+ "originDatasets": [
+ {
+ "filename": "LB (Amygdala) [v6.4, ICBM 2009c Asymmetric, left hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "fa4cab6a-1cec-4cec-b481-90aa0cc7d96c"
+ }
+ ],
"fullId": {
"kg": {
"kgSchema": "minds/core/parcellationregion/v1.0.0",
"kgId": "708df0fa-e9a4-4c23-bd85-8957f6d30faf"
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- "filename": "LB (Amygdala) [v6.4, ICBM 2009c Asymmetric, left hemisphere]"
+ "_": {
+ "xml": {
+ "name": "LB (Amygdala)",
+ "id": "187",
+ "grayvalue": "91"
+ },
+ "dat": {
+ "colors": false,
+ "names": false
}
- ],
- "ontologyLabelIndex": 187
+ }
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{
"name": "LB (Amygdala)",
- "arealabel": "LB",
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- "labelIndex": 90,
- "doi": "https://doi.org/10.25493/C3X0-NV3",
- "synonyms": [],
- "rgb": null,
- "children": [],
+ "labelIndex": 91,
+ "rgb": [
+ 200,
+ 200,
+ 200
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+ "ngId": "ICBM152_V24_RIGHT_NG",
+ "originDatasets": [
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+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "fa4cab6a-1cec-4cec-b481-90aa0cc7d96c"
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- "filename": "LB (Amygdala) [v6.4, ICBM 2009c Asymmetric, right hemisphere]"
+ "_": {
+ "xml": {
+ "name": "LB (Amygdala)",
+ "id": "187",
+ "grayvalue": "91"
+ },
+ "dat": {
+ "colors": false,
+ "names": false
}
- ],
- "ontologyLabelIndex": 187
+ }
}
],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "708df0fa-e9a4-4c23-bd85-8957f6d30faf"
+ "_": {
+ "jubrain-ontology_24.json": {
+ "name": "LB (Amygdala)",
+ "arealabel": "LB",
+ "status": "publicP",
+ "labelIndex": "187",
+ "doi": "https://doi.org/10.25493/C3X0-NV3",
+ "synonyms": [],
+ "rgb": null,
+ "kgHref": "https://kg.ebrains.eu/search/instances/Dataset/fa4cab6a-1cec-4cec-b481-90aa0cc7d96c"
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+ "kgRegion": {
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diff --git a/src/res/ext/MNI152NehubaConfig.json b/src/res/ext/MNI152NehubaConfig.json
index 8e8a4d486d846ee394940a2504fcdcd2029dd2eb..13084b6ed79d8998eea03e1331ddcada26f2d0c4 100644
--- a/src/res/ext/MNI152NehubaConfig.json
+++ b/src/res/ext/MNI152NehubaConfig.json
@@ -157,7 +157,7 @@
},
"julich brain mni152 v22 left": {
"type": "segmentation",
- "visible": true,
+ "visible": false,
"source": "precomputed://https://neuroglancer-dev.humanbrainproject.org/precomputed/data-repo/20200807_julich_brain_v2_mni152_left/precomputed",
"transform": [
[
@@ -188,7 +188,7 @@
},
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"type": "segmentation",
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+ "visible": false,
"source": "precomputed://https://neuroglancer-dev.humanbrainproject.org/precomputed/data-repo/20200807_julich_brain_v2_mni152_right/precomputed",
"transform": [
[
@@ -217,6 +217,74 @@
]
]
},
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+ "visible": true,
+ "source": "precomputed://https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20201002_JulichBrain-V2_4-ICBM152_MPM_mesh/precomputed/left",
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+ }
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"fibre bundle long": {
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diff --git a/src/res/ext/colin.json b/src/res/ext/colin.json
index 736b152ad086a6dbf0a9e8053528df84a6ab1909..5d151d6c502b5b6975039f65ac9a0f3f97ed680f 100644
--- a/src/res/ext/colin.json
+++ b/src/res/ext/colin.json
@@ -1010,9 +1010,9 @@
"status": "left hemisphere",
"labelIndex": 95,
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@@ -1045,9 +1045,9 @@
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