see viewer link: https://siibra-explorer-rc.apps.jsc.hbp.eu/
Generated checklist
name | validator | validation |
---|---|---|
see viewer link: https://siibra-explorer-rc.apps.jsc.hbp.eu/
Generated checklist
name | validator | validation |
---|---|---|
Ahmet Nihat Simsek (4db4c70f) at 20 Feb 13:51
Remove Julich Brain 3.1 prerelease for config release
Ahmet Nihat Simsek (8ae31075) at 20 Feb 13:51
Remove Julich Brain 3.1 prerelease for config release
maint: updated voi def
Please do not merge before reviewing.
as of siibra-0.4a51
While doing some upkeeping in siibra-explorer, I noticed quite a few regions under parcellation having the exact name.[1]
They fall in the following categories:
More worryingly, some maps seems to have the duplicated name, too. (see https://jugit.fz-juelich.de/t.dickscheid/brainscapes-configurations/-/blob/siibra-0.4a51/maps/mni152-difumo1024-labelled.json#L997-1002 and https://jugit.fz-juelich.de/t.dickscheid/brainscapes-configurations/-/blob/siibra-0.4a51/maps/mni152-difumo1024-labelled.json#L1903-1908 . There are almost certainly other examples.
[1] full list of regions that contain duplicated name
DuplicatedErr(filename='parcellations/difumo512.json', key='Cerebellum Crus II')
DuplicatedErr(filename='parcellations/difumo512.json', key='Cerebellum VIIb')
DuplicatedErr(filename='parcellations/difumo512.json', key='Cerebellum V')
DuplicatedErr(filename='parcellations/difumo512.json', key='Cerebellum VI anterior')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum Crus I - left hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum VI')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum VI')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum VIIb')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum Crus I - right hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum VI - left hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum IX')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum Crus II')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum IV')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum VI - left hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum Crus I - left hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum IV')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum Crus I - right hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum Crus I - left hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum VI')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum Crus II')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum IV')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum IV')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum V')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum V')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum Crus I - left hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum IX')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum VI - right hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum Crus I - right hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum IX')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum V')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum V')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum Crus II - left hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum VI - right hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum VIIb')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum VI - left hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum V - right hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum Crus I - right hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum VI - right hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum Crus I - left hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum VI - left hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum Crus II - right hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum VI - right hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum VI')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum Crus I - right hemisphere')
DuplicatedErr(filename='parcellations/difumo1024.json', key='Cerebellum IX')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Caudal Middle Frontal - Precuneus')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Caudal Middle Frontal - Precentral')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Caudal Middle Frontal – Rostral Middle Frontal')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Caudal Middle Frontal – Superior Frontal')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Fusiform – Lateral Occipital')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Isthmus Cingulate - Precuneus')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Inferior Parietal – Lateral Occipital')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Inferior Parietal - Supramarginal')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Inferior Temporal – Middle Temporal')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Lateral Orbitofrontal – Rostral Middle Frontal')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Lateral Orbitofrontal – Superior Temporal')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Middle Orbitofrontal – Superior Temporal')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Middle Temporal - Supramarginal')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Middle Temporal – Superior Temporal')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Pars Opercularis - Insula')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Pars Opercularis – Superior Frontal')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Pars Orbitalis - Insula')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Posterior Cingulate – Rostral Anterior Cingulate')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Poscentral - Precentral')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Precentral - Insula')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Rostral Middle Frontal – Superior Frontal')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Supramarginal - Insula')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Superior Parietal - Supramarginal')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Superior Temporal – Transverse Temporal')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Pars Triangularis - Insula')
DuplicatedErr(filename='parcellations/bundles_short.json', key='Pars Triangularis – Superior Frontal')
DuplicatedErr(filename='parcellations/julichbrain_v1_18.json', key='Ch 123 (Basal Forebrain)')
DuplicatedErr(filename='parcellations/julichbrain_v1_18.json', key='Ch 123 (Basal Forebrain) - left hemisphere')
DuplicatedErr(filename='parcellations/julichbrain_v1_18.json', key='Ch 123 (Basal Forebrain) - right hemisphere')
DuplicatedErr(filename='parcellations/julichbrain_v1_18.json', key='CM (Amygdala)')
DuplicatedErr(filename='parcellations/julichbrain_v1_18.json', key='CM (Amygdala) - left hemisphere')
DuplicatedErr(filename='parcellations/julichbrain_v1_18.json', key='CM (Amygdala) - right hemisphere')
DuplicatedErr(filename='parcellations/julichbrain_v1_18.json', key='Interposed Nucleus (Cerebellum)')
DuplicatedErr(filename='parcellations/julichbrain_v1_18.json', key='Interposed Nucleus (Cerebellum) - left hemisphere')
DuplicatedErr(filename='parcellations/julichbrain_v1_18.json', key='Interposed Nucleus (Cerebellum) - right hemisphere')
DuplicatedErr(filename='parcellations/julichbrain_v2_9_0.json', key='Ch 123 (Basal Forebrain)')
DuplicatedErr(filename='parcellations/julichbrain_v2_9_0.json', key='Ch 123 (Basal Forebrain) - left hemisphere')
DuplicatedErr(filename='parcellations/julichbrain_v2_9_0.json', key='Ch 123 (Basal Forebrain) - right hemisphere')
DuplicatedErr(filename='parcellations/julichbrain_v2_9_0.json', key='Interposed Nucleus (Cerebellum)')
DuplicatedErr(filename='parcellations/julichbrain_v2_9_0.json', key='Interposed Nucleus (Cerebellum) - left hemisphere')
DuplicatedErr(filename='parcellations/julichbrain_v2_9_0.json', key='Interposed Nucleus (Cerebellum) - right hemisphere')
DuplicatedErr(filename='parcellations/julichbrain_v3_0_2.json', key='Temporal-to-Parietal')
DuplicatedErr(filename='parcellations/julichbrain_v3_0_2.json', key='Frontal-to-Temporal')
DuplicatedErr(filename='parcellations/julichbrain_v3_0_2.json', key='Frontal-to-Occipital')
DuplicatedErr(filename='parcellations/difumo256.json', key='Cerebellum Crus II')
DuplicatedErr(filename='parcellations/difumo256.json', key='Cerebellum VIIb')
DuplicatedErr(filename='parcellations/difumo256.json', key='Cerebellum V')
DuplicatedErr(filename='parcellations/difumo256.json', key='Cerebellum VI anterior')
as of siibra-0.4a51
allen ccf v3 template is at https://neuroglancer.humanbrainproject.eu/precomputed/AMBA/templates/v3/stpt
The transform
curl -L https://neuroglancer.humanbrainproject.eu/precomputed/AMBA/templates/v3/stpt/transform.json | jq
prints out to be
[
[
1,
0,
0,
-5737500
],
[
0,
1,
0,
-6637500
],
[
0,
0,
1,
-4037500
],
[
0,
0,
0,
1
]
]
Accounting for half voxel shift, (full voxel is 25um) the translation in um ends up being:
[ 5725, 6625, 4025 ]
Total volume size (in um), according to the neuroglancer info, is
[ 11400, 13200, 8000 ]
This means, where we regard as [0, 0, 0 ] is exactly shifted 1 voxel to the RAS direction.
This can be verified in the viewer. at [0, 0, Z], the viewer is not at the center of the brain, as far as left right hemisphere is concerned:
Here is what I propose:
What impact does this fix have:
The support for KG v1 has ended. The connection will be removed from siibra-python as well. We need to replace all the references to v1 or makes sure there is reference to v3 as well (preferably Ebrains DatasetVersion)