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refactor: use attributes #53

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refactor: use attributes #53

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8d4b417
feat: updated most features (ex. connectivity, bold)
xgui3783 May 23, 2024
64fb5dd
feat: updated space to new schema
xgui3783 May 23, 2024
d15ad22
convert parcellations to attribute system
AhmetNSimsek May 23, 2024
4935823
fix: archive_options
xgui3783 May 23, 2024
56e6e27
fix: publication -> url/doi
xgui3783 May 23, 2024
20c025d
fix: space publication
xgui3783 May 24, 2024
b53f914
fix: dx.doi.org -> doi.org
xgui3783 May 24, 2024
c10f202
fix archive schema
xgui3783 May 27, 2024
0c81587
refactor: converted cnmtx to ecs
xgui3783 May 29, 2024
4d9fc4d
readd shortnames for spaces
AhmetNSimsek Jun 5, 2024
4d977ac
cell density: added aggregate by
xgui3783 Jun 7, 2024
77016e6
fix space_id in layerboundary
xgui3783 Jun 7, 2024
b23b8b0
convert maps to attribute system
AhmetNSimsek Jun 11, 2024
8c74629
Revert "convert maps to attribute system"
AhmetNSimsek Jun 12, 2024
a2831be
visf atlas: remove temp provider in data-proxy
AhmetNSimsek Jun 12, 2024
97ed4a0
convert maps to attribute system
AhmetNSimsek Jun 13, 2024
a203a84
Revert "convert maps to attribute system"
AhmetNSimsek Jun 13, 2024
69e7640
convert maps to attribute system
AhmetNSimsek Jun 13, 2024
0402df2
fix: aggregate by
xgui3783 Jun 13, 2024
d2c2626
fix icbm zip file
xgui3783 Jun 14, 2024
f7f324f
fix: add matrix to connectivity data
xgui3783 Jun 17, 2024
5e31a4c
correct version value for jba 3.1
AhmetNSimsek Jun 24, 2024
aaa50c5
Use mesh attributes for volumes with mesh format
AhmetNSimsek Jul 2, 2024
35fb6f1
Revert map config conversion to attribute system
AhmetNSimsek Jul 3, 2024
02c0f98
Update jba3.1 prerelase to EBRAINS release version
AhmetNSimsek Jul 3, 2024
690b438
reconvert jba 3.1 and 3.0.3 parc configs to attribute collection
AhmetNSimsek Jul 3, 2024
4d3f215
Convert maps to attribute collection
AhmetNSimsek Jul 3, 2024
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feat: updated space to new schema
  • Loading branch information
@xgui3783
xgui3783 committed May 23, 2024
commit 64fb5ddd0e4fb75c805334648757ce924e984e3a
75 changes: 50 additions & 25 deletions spaces/bigbrain_2015.json
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Original file line number Diff line number Diff line change
@@ -1,27 +1,52 @@
{
"@id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
"@type": "siibra/space/v0.0.1",
"name": "BigBrain microscopic template (histology)",
"shortName": "BigBrain",
"modality": "histology",
"species": "homo sapiens",
"volumes": [
{
"@type": "siibra/volume/v0.0.1",
"providers": {
"neuroglancer/precomputed": "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/8bit",
"neuroglancer/precompmesh/surface": "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/classif_mesh 100"
}
}
],
"ebrains": {
"openminds/Species": "97c070c6-8e1f-4ee8-9d28-18c7945921dd",
"openminds/DatasetVersion": "d07f9305-1e75-4548-a348-b155fb323d31"
},
"publications": [
{
"citation": "Amunts, K., Lepage, C., Borgeat, L., Mohlberg, H., Dickscheid, T., Rousseau, M.-É., Bludau, S., Bazin, P.-L., Lewis, L. B., Oros-Peusquens, A.-M., Shah, N. J., Lippert, T., Zilles, K., & Evans, A. C. (2013). BigBrain: An Ultrahigh-Resolution 3D Human Brain Model. Science, 340(6139), 1472-1475. https://doi.org/10.1126/science.1235381",
"url": "https://doi.org/10.1126/science.1235381"
}
]
"@type": "siibra/atlases/space/v0.1",
"attributes": [
{
"@type": "x-siibra/tmp",
"publications": [
{
"citation": "Amunts, K., Lepage, C., Borgeat, L., Mohlberg, H., Dickscheid, T., Rousseau, M.-\u00c9., Bludau, S., Bazin, P.-L., Lewis, L. B., Oros-Peusquens, A.-M., Shah, N. J., Lippert, T., Zilles, K., & Evans, A. C. (2013). BigBrain: An Ultrahigh-Resolution 3D Human Brain Model. Science, 340(6139), 1472-1475. https://doi.org/10.1126/science.1235381",
"url": "https://doi.org/10.1126/science.1235381"
}
]
},
{
"@type": "siibra/attr/desc/id/v0.1",
"value": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588"
},
{
"@type": "siibra/attr/desc/name/v0.1",
"value": "BigBrain microscopic template (histology)"
},
{
"@type": "siibra/attr/desc/speciesspec/v0.1",
"value": "homo sapiens"
},
{
"@type": "siibra/attr/desc/modality/v0.1",
"value": "histology"
},
{
"@type": "siibra/attr/desc/ebrains/v0.1",
"ids": {
"openminds/Species": "97c070c6-8e1f-4ee8-9d28-18c7945921dd",
"openminds/DatasetVersion": "d07f9305-1e75-4548-a348-b155fb323d31"
}
},
{
"@type": "siibra/attr/data/image/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
"format": "neuroglancer/precomputed",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/8bit"
},
{
"@type": "siibra/attr/data/image/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
"format": "neuroglancer/precompmesh",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/classif_mesh",
"archive": {
"label": 100
}
}
]
}
141 changes: 87 additions & 54 deletions spaces/fsaverage.json
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Original file line number Diff line number Diff line change
@@ -1,56 +1,89 @@
{
"@id": "minds/core/referencespace/v1.0.0/tmp-fsaverage",
"@type": "siibra/space/v0.0.1",
"name": "freesurfer fsaverage",
"shortName": "fsaverage",
"modality": "surface",
"species": "homo sapiens",
"ebrains": {
"openminds/Species": "97c070c6-8e1f-4ee8-9d28-18c7945921dd"
},
"volumes": [
{
"@type": "siibra/volume/v0.0.1",
"variant": "white matter",
"providers": {
"gii-mesh": {
"left hemisphere": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/fsaverage/fsaverage/lh.white.gii",
"right hemisphere": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/fsaverage/fsaverage/rh.white.gii"
}
}
},
{
"@type": "siibra/volume/v0.0.1",
"fragment": "left hemisphere",
"variant": "pial",
"providers": {
"gii-mesh": {
"left hemisphere": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/fsaverage/fsaverage/lh.pial.gii",
"right hemisphere": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/fsaverage/fsaverage/rh.pial.gii"
}
}
},
{
"@type": "siibra/volume/v0.0.1",
"fragment": "left hemisphere",
"variant": "inflated",
"providers": {
"gii-mesh": {
"left hemisphere": "https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20210415-new-freesurfer/fsa7-translated-inflated/lh.inflated.surf.gii",
"right hemisphere": "https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20210415-new-freesurfer/fsa7-translated-inflated/rh.inflated.surf.gii"
}
}
}
],
"publications": [
{
"name": "FreeSurfer",
"url": "https://10.1016/j.neuroimage.2012.01.021",
"authors": [
"Bruce Fischl"
],
"description": "FreeSurfer is a suite of tools for the analysis of neuroimaging data that provides an array of algorithms to quantify the functional, connectional and structural properties of the human brain. It has evolved from a package primarily aimed at generating surface representations of the cerebral cortex into one that automatically creates models of most macroscopically visible structures in the human brain given any reasonable T1-weighted input image. It is freely available, runs on a wide variety of hardware and software platforms, and is open source.",
"citation": "Fischl B. FreeSurfer. Neuroimage. 2012 Aug 15;62(2):774-81. doi: 10.1016/j.neuroimage.2012.01.021. Epub 2012 Jan 10. PMID: 22248573; PMCID: PMC3685476."
}
]
"@type": "siibra/atlases/space/v0.1",
"attributes": [
{
"@type": "x-siibra/tmp",
"publications": [
{
"name": "FreeSurfer",
"url": "https://10.1016/j.neuroimage.2012.01.021",
"authors": [
"Bruce Fischl"
],
"description": "FreeSurfer is a suite of tools for the analysis of neuroimaging data that provides an array of algorithms to quantify the functional, connectional and structural properties of the human brain. It has evolved from a package primarily aimed at generating surface representations of the cerebral cortex into one that automatically creates models of most macroscopically visible structures in the human brain given any reasonable T1-weighted input image. It is freely available, runs on a wide variety of hardware and software platforms, and is open source.",
"citation": "Fischl B. FreeSurfer. Neuroimage. 2012 Aug 15;62(2):774-81. doi: 10.1016/j.neuroimage.2012.01.021. Epub 2012 Jan 10. PMID: 22248573; PMCID: PMC3685476."
}
]
},
{
"@type": "siibra/attr/desc/id/v0.1",
"value": "minds/core/referencespace/v1.0.0/tmp-fsaverage"
},
{
"@type": "siibra/attr/desc/name/v0.1",
"value": "freesurfer fsaverage"
},
{
"@type": "siibra/attr/desc/speciesspec/v0.1",
"value": "homo sapiens"
},
{
"@type": "siibra/attr/desc/modality/v0.1",
"value": "surface"
},
{
"@type": "siibra/attr/desc/ebrains/v0.1",
"ids": {
"openminds/Species": "97c070c6-8e1f-4ee8-9d28-18c7945921dd"
}
},
{
"@type": "siibra/attr/data/image/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/tmp-fsaverage",
"format": "gii-mesh",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/fsaverage/fsaverage/lh.white.gii",
"x-siibra/volume-variant": "white matter",
"x-siibra/volume-fragment": "left hemisphere"
},
{
"@type": "siibra/attr/data/image/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/tmp-fsaverage",
"format": "gii-mesh",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/fsaverage/fsaverage/rh.white.gii",
"x-siibra/volume-variant": "white matter",
"x-siibra/volume-fragment": "right hemisphere"
},
{
"@type": "siibra/attr/data/image/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/tmp-fsaverage",
"format": "gii-mesh",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/fsaverage/fsaverage/lh.pial.gii",
"x-siibra/volume-variant": "pial",
"x-siibra/volume-fragment": "left hemisphere"
},
{
"@type": "siibra/attr/data/image/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/tmp-fsaverage",
"format": "gii-mesh",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/fsaverage/fsaverage/rh.pial.gii",
"x-siibra/volume-variant": "pial",
"x-siibra/volume-fragment": "right hemisphere"
},
{
"@type": "siibra/attr/data/image/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/tmp-fsaverage",
"format": "gii-mesh",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20210415-new-freesurfer/fsa7-translated-inflated/lh.inflated.surf.gii",
"x-siibra/volume-variant": "inflated",
"x-siibra/volume-fragment": "left hemisphere"
},
{
"@type": "siibra/attr/data/image/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/tmp-fsaverage",
"format": "gii-mesh",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20210415-new-freesurfer/fsa7-translated-inflated/rh.inflated.surf.gii",
"x-siibra/volume-variant": "inflated",
"x-siibra/volume-fragment": "right hemisphere"
}
]
}
139 changes: 87 additions & 52 deletions spaces/fsaverage6.json
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Original file line number Diff line number Diff line change
@@ -1,54 +1,89 @@
{
"@id": "minds/core/referencespace/v1.0.0/tmp-fsaverage6",
"@type": "siibra/space/v0.0.1",
"name": "freesurfer fsaverage6",
"shortName": "fsaverage6",
"modality": "surface",
"species": "homo sapiens",
"ebrains": {
"openminds/Species": "97c070c6-8e1f-4ee8-9d28-18c7945921dd"
},
"volumes": [
{
"@type": "siibra/volume/v0.0.1",
"variant": "white matter",
"providers": {
"gii-mesh": {
"left hemisphere": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/fsaverage/fsaverage6/lh.white.gii",
"right hemisphere": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/fsaverage/fsaverage6/rh.white.gii"
}
}
},
{
"@type": "siibra/volume/v0.0.1",
"variant": "pial",
"providers": {
"gii-mesh": {
"left hemisphere": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/fsaverage/fsaverage6/lh.pial.gii",
"right hemisphere": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/fsaverage/fsaverage6/rh.pial.gii"
}
}
},
{
"@type": "siibra/volume/v0.0.1",
"variant": "inflated",
"providers": {
"gii-mesh": {
"left hemisphere": "https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20210415-new-freesurfer/fsa6-translated-inflated/lh.inflated.surf.gii",
"right hemisphere": "https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20210415-new-freesurfer/fsa6-translated-inflated/rh.inflated.surf.gii"
}
}
}
],
"publications": [
{
"name": "FreeSurfer",
"url": "https://10.1016/j.neuroimage.2012.01.021",
"authors": [
"Bruce Fischl"
],
"description": "FreeSurfer is a suite of tools for the analysis of neuroimaging data that provides an array of algorithms to quantify the functional, connectional and structural properties of the human brain. It has evolved from a package primarily aimed at generating surface representations of the cerebral cortex into one that automatically creates models of most macroscopically visible structures in the human brain given any reasonable T1-weighted input image. It is freely available, runs on a wide variety of hardware and software platforms, and is open source.",
"citation": "Fischl B. FreeSurfer. Neuroimage. 2012 Aug 15;62(2):774-81. doi: 10.1016/j.neuroimage.2012.01.021. Epub 2012 Jan 10. PMID: 22248573; PMCID: PMC3685476."
}
]
"@type": "siibra/atlases/space/v0.1",
"attributes": [
{
"@type": "x-siibra/tmp",
"publications": [
{
"name": "FreeSurfer",
"url": "https://10.1016/j.neuroimage.2012.01.021",
"authors": [
"Bruce Fischl"
],
"description": "FreeSurfer is a suite of tools for the analysis of neuroimaging data that provides an array of algorithms to quantify the functional, connectional and structural properties of the human brain. It has evolved from a package primarily aimed at generating surface representations of the cerebral cortex into one that automatically creates models of most macroscopically visible structures in the human brain given any reasonable T1-weighted input image. It is freely available, runs on a wide variety of hardware and software platforms, and is open source.",
"citation": "Fischl B. FreeSurfer. Neuroimage. 2012 Aug 15;62(2):774-81. doi: 10.1016/j.neuroimage.2012.01.021. Epub 2012 Jan 10. PMID: 22248573; PMCID: PMC3685476."
}
]
},
{
"@type": "siibra/attr/desc/id/v0.1",
"value": "minds/core/referencespace/v1.0.0/tmp-fsaverage6"
},
{
"@type": "siibra/attr/desc/name/v0.1",
"value": "freesurfer fsaverage6"
},
{
"@type": "siibra/attr/desc/speciesspec/v0.1",
"value": "homo sapiens"
},
{
"@type": "siibra/attr/desc/modality/v0.1",
"value": "surface"
},
{
"@type": "siibra/attr/desc/ebrains/v0.1",
"ids": {
"openminds/Species": "97c070c6-8e1f-4ee8-9d28-18c7945921dd"
}
},
{
"@type": "siibra/attr/data/image/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/tmp-fsaverage6",
"format": "gii-mesh",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/fsaverage/fsaverage6/lh.white.gii",
"x-siibra/volume-variant": "white matter",
"x-siibra/volume-fragment": "left hemisphere"
},
{
"@type": "siibra/attr/data/image/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/tmp-fsaverage6",
"format": "gii-mesh",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/fsaverage/fsaverage6/rh.white.gii",
"x-siibra/volume-variant": "white matter",
"x-siibra/volume-fragment": "right hemisphere"
},
{
"@type": "siibra/attr/data/image/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/tmp-fsaverage6",
"format": "gii-mesh",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/fsaverage/fsaverage6/lh.pial.gii",
"x-siibra/volume-variant": "pial",
"x-siibra/volume-fragment": "left hemisphere"
},
{
"@type": "siibra/attr/data/image/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/tmp-fsaverage6",
"format": "gii-mesh",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/fsaverage/fsaverage6/rh.pial.gii",
"x-siibra/volume-variant": "pial",
"x-siibra/volume-fragment": "right hemisphere"
},
{
"@type": "siibra/attr/data/image/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/tmp-fsaverage6",
"format": "gii-mesh",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20210415-new-freesurfer/fsa6-translated-inflated/lh.inflated.surf.gii",
"x-siibra/volume-variant": "inflated",
"x-siibra/volume-fragment": "left hemisphere"
},
{
"@type": "siibra/attr/data/image/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/tmp-fsaverage6",
"format": "gii-mesh",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20210415-new-freesurfer/fsa6-translated-inflated/rh.inflated.surf.gii",
"x-siibra/volume-variant": "inflated",
"x-siibra/volume-fragment": "right hemisphere"
}
]
}
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