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tests/testthat/_snaps/ggseg_atlas.md
In ggseg.formats: Brain Atlas Data Structures for the 'ggsegverse' Ecosystem
ggseg_atlas class / print method works
Code
print(dk())
Message
-- dk ggseg atlas --------------------------------------------------------------
Type: cortical
Regions: 35
Hemispheres: left, right
Views: inferior, lateral, superior, medial
Palette: v
Rendering: v ggseg
v ggseg3d (vertices)
--------------------------------------------------------------------------------
Output
hemi region label
1 left banks of superior temporal sulcus lh_bankssts
2 left caudal anterior cingulate lh_caudalanteriorcingulate
3 left caudal middle frontal lh_caudalmiddlefrontal
4 left corpus callosum lh_corpuscallosum
5 left cuneus lh_cuneus
6 left entorhinal lh_entorhinal
7 left fusiform lh_fusiform
8 left inferior parietal lh_inferiorparietal
9 left inferior temporal lh_inferiortemporal
10 left isthmus cingulate lh_isthmuscingulate
lobe
1 temporal
2 cingulate
3 frontal
4 white matter
5 occipital
6 temporal
7 temporal
8 parietal
9 temporal
10 cingulate
Message
... with 60 more rows
ggseg_atlas class / print caps core rows at n
Code
print(dk(), n = 3)
Message
-- dk ggseg atlas --------------------------------------------------------------
Type: cortical
Regions: 35
Hemispheres: left, right
Views: inferior, lateral, superior, medial
Palette: v
Rendering: v ggseg
v ggseg3d (vertices)
--------------------------------------------------------------------------------
Output
hemi region label lobe
1 left banks of superior temporal sulcus lh_bankssts temporal
2 left caudal anterior cingulate lh_caudalanteriorcingulate cingulate
3 left caudal middle frontal lh_caudalmiddlefrontal frontal
Message
... with 67 more rows
Code
print(dk(), n = 6)
Message
-- dk ggseg atlas --------------------------------------------------------------
Type: cortical
Regions: 35
Hemispheres: left, right
Views: inferior, lateral, superior, medial
Palette: v
Rendering: v ggseg
v ggseg3d (vertices)
--------------------------------------------------------------------------------
Output
hemi region label
1 left banks of superior temporal sulcus lh_bankssts
2 left caudal anterior cingulate lh_caudalanteriorcingulate
3 left caudal middle frontal lh_caudalmiddlefrontal
4 left corpus callosum lh_corpuscallosum
5 left cuneus lh_cuneus
6 left entorhinal lh_entorhinal
lobe
1 temporal
2 cingulate
3 frontal
4 white matter
5 occipital
6 temporal
Message
... with 64 more rows
print.ggseg_atlas rendering branches / prints a tract atlas (centerlines)
Code
print(tracula())
Message
-- tracula ggseg atlas ---------------------------------------------------------
Type: tract
Regions: 26
Hemispheres: midline, left, right
Views: axial_2, axial_4, coronal_3, coronal_4, sagittal_midline, sagittal_left,
sagittal_right
Palette: v
Rendering: v ggseg
v ggseg3d (centerlines)
--------------------------------------------------------------------------------
Output
hemi region label group
1 midline anterior commissure acomm.bbr.prep commissure
2 midline CC body central cc.bodyc.bbr.prep corpus callosum
3 midline CC body parietal cc.bodyp.bbr.prep corpus callosum
4 midline CC body prefrontal cc.bodypf.bbr.prep corpus callosum
5 midline CC body premotor cc.bodypm.bbr.prep corpus callosum
6 midline CC body temporal cc.bodyt.bbr.prep corpus callosum
7 midline CC genu cc.genu.bbr.prep corpus callosum
8 midline CC rostrum cc.rostrum.bbr.prep corpus callosum
9 midline CC splenium cc.splenium.bbr.prep corpus callosum
10 left arcuate fasciculus lh.af.bbr.prep association
Message
... with 32 more rows
print.ggseg_atlas rendering branches / prints a subcortical atlas (meshes)
Code
print(aseg())
Message
-- aseg ggseg atlas ------------------------------------------------------------
Type: subcortical
Regions: 19
Hemispheres: left, NA, right
Views: axial_3, axial_4, axial_5, sagittal, axial_6, coronal_1, coronal_2
Palette: v
Rendering: v ggseg
v ggseg3d (meshes)
--------------------------------------------------------------------------------
Output
hemi region label structure
1 left Cerebellum Left-Cerebellum-Cortex cerebellum
2 left Cerebellum Left-Cerebellum-Cortex cerebellum
3 left Thalamus Left-Thalamus basal ganglia
4 left Thalamus Left-Thalamus basal ganglia
5 left Thalamus Proper Left-Thalamus basal ganglia
6 left Thalamus Proper Left-Thalamus basal ganglia
7 left Caudate Left-Caudate basal ganglia
8 left Caudate Left-Caudate basal ganglia
9 left Putamen Left-Putamen basal ganglia
10 left Putamen Left-Putamen basal ganglia
Message
... with 37 more rows
print.ggseg_atlas rendering branches / prints a cortical atlas (vertices)
Code
print(dk())
Message
-- dk ggseg atlas --------------------------------------------------------------
Type: cortical
Regions: 35
Hemispheres: left, right
Views: inferior, lateral, superior, medial
Palette: v
Rendering: v ggseg
v ggseg3d (vertices)
--------------------------------------------------------------------------------
Output
hemi region label
1 left banks of superior temporal sulcus lh_bankssts
2 left caudal anterior cingulate lh_caudalanteriorcingulate
3 left caudal middle frontal lh_caudalmiddlefrontal
4 left corpus callosum lh_corpuscallosum
5 left cuneus lh_cuneus
6 left entorhinal lh_entorhinal
7 left fusiform lh_fusiform
8 left inferior parietal lh_inferiorparietal
9 left inferior temporal lh_inferiortemporal
10 left isthmus cingulate lh_isthmuscingulate
lobe
1 temporal
2 cingulate
3 frontal
4 white matter
5 occipital
6 temporal
7 temporal
8 parietal
9 temporal
10 cingulate
Message
... with 60 more rows
print.ggseg_atlas rendering branches / prints an atlas with no 3D geometry as none
Code
print(atlas)
Message
-- test ggseg atlas ------------------------------------------------------------
Type: cerebellar
Regions: 1
Hemispheres: left
Views: lateral
Palette: x
Rendering: v ggseg
x ggseg3d (none)
--------------------------------------------------------------------------------
Output
hemi region label
1 left frontal lh_frontal
print.ggseg_atlas rendering branches / prints a polygon atlas summary with views
Code
print(poly_atlas)
Message
-- dk ggseg atlas --------------------------------------------------------------
Type: cortical
Regions: 35
Hemispheres: left, right
Views: inferior, lateral, superior, medial
Palette: v
Rendering: v ggseg
v ggseg3d (vertices)
--------------------------------------------------------------------------------
Output
hemi region label
1 left banks of superior temporal sulcus lh_bankssts
2 left caudal anterior cingulate lh_caudalanteriorcingulate
3 left caudal middle frontal lh_caudalmiddlefrontal
4 left corpus callosum lh_corpuscallosum
5 left cuneus lh_cuneus
6 left entorhinal lh_entorhinal
7 left fusiform lh_fusiform
8 left inferior parietal lh_inferiorparietal
9 left inferior temporal lh_inferiortemporal
10 left isthmus cingulate lh_isthmuscingulate
lobe
1 temporal
2 cingulate
3 frontal
4 white matter
5 occipital
6 temporal
7 temporal
8 parietal
9 temporal
10 cingulate
Message
... with 60 more rows
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ggseg_atlas class / print method works
Code
print(dk())
Message
-- dk ggseg atlas --------------------------------------------------------------
Type: cortical
Regions: 35
Hemispheres: left, right
Views: inferior, lateral, superior, medial
Palette: v
Rendering: v ggseg
v ggseg3d (vertices)
--------------------------------------------------------------------------------
Output
hemi region label
1 left banks of superior temporal sulcus lh_bankssts
2 left caudal anterior cingulate lh_caudalanteriorcingulate
3 left caudal middle frontal lh_caudalmiddlefrontal
4 left corpus callosum lh_corpuscallosum
5 left cuneus lh_cuneus
6 left entorhinal lh_entorhinal
7 left fusiform lh_fusiform
8 left inferior parietal lh_inferiorparietal
9 left inferior temporal lh_inferiortemporal
10 left isthmus cingulate lh_isthmuscingulate
lobe
1 temporal
2 cingulate
3 frontal
4 white matter
5 occipital
6 temporal
7 temporal
8 parietal
9 temporal
10 cingulate
Message
... with 60 more rows
ggseg_atlas class / print caps core rows at n
Code
print(dk(), n = 3)
Message
-- dk ggseg atlas --------------------------------------------------------------
Type: cortical
Regions: 35
Hemispheres: left, right
Views: inferior, lateral, superior, medial
Palette: v
Rendering: v ggseg
v ggseg3d (vertices)
--------------------------------------------------------------------------------
Output
hemi region label lobe
1 left banks of superior temporal sulcus lh_bankssts temporal
2 left caudal anterior cingulate lh_caudalanteriorcingulate cingulate
3 left caudal middle frontal lh_caudalmiddlefrontal frontal
Message
... with 67 more rows
Code
print(dk(), n = 6)
Message
-- dk ggseg atlas --------------------------------------------------------------
Type: cortical
Regions: 35
Hemispheres: left, right
Views: inferior, lateral, superior, medial
Palette: v
Rendering: v ggseg
v ggseg3d (vertices)
--------------------------------------------------------------------------------
Output
hemi region label
1 left banks of superior temporal sulcus lh_bankssts
2 left caudal anterior cingulate lh_caudalanteriorcingulate
3 left caudal middle frontal lh_caudalmiddlefrontal
4 left corpus callosum lh_corpuscallosum
5 left cuneus lh_cuneus
6 left entorhinal lh_entorhinal
lobe
1 temporal
2 cingulate
3 frontal
4 white matter
5 occipital
6 temporal
Message
... with 64 more rows
print.ggseg_atlas rendering branches / prints a tract atlas (centerlines)
Code
print(tracula())
Message
-- tracula ggseg atlas ---------------------------------------------------------
Type: tract
Regions: 26
Hemispheres: midline, left, right
Views: axial_2, axial_4, coronal_3, coronal_4, sagittal_midline, sagittal_left,
sagittal_right
Palette: v
Rendering: v ggseg
v ggseg3d (centerlines)
--------------------------------------------------------------------------------
Output
hemi region label group
1 midline anterior commissure acomm.bbr.prep commissure
2 midline CC body central cc.bodyc.bbr.prep corpus callosum
3 midline CC body parietal cc.bodyp.bbr.prep corpus callosum
4 midline CC body prefrontal cc.bodypf.bbr.prep corpus callosum
5 midline CC body premotor cc.bodypm.bbr.prep corpus callosum
6 midline CC body temporal cc.bodyt.bbr.prep corpus callosum
7 midline CC genu cc.genu.bbr.prep corpus callosum
8 midline CC rostrum cc.rostrum.bbr.prep corpus callosum
9 midline CC splenium cc.splenium.bbr.prep corpus callosum
10 left arcuate fasciculus lh.af.bbr.prep association
Message
... with 32 more rows
print.ggseg_atlas rendering branches / prints a subcortical atlas (meshes)
Code
print(aseg())
Message
-- aseg ggseg atlas ------------------------------------------------------------
Type: subcortical
Regions: 19
Hemispheres: left, NA, right
Views: axial_3, axial_4, axial_5, sagittal, axial_6, coronal_1, coronal_2
Palette: v
Rendering: v ggseg
v ggseg3d (meshes)
--------------------------------------------------------------------------------
Output
hemi region label structure
1 left Cerebellum Left-Cerebellum-Cortex cerebellum
2 left Cerebellum Left-Cerebellum-Cortex cerebellum
3 left Thalamus Left-Thalamus basal ganglia
4 left Thalamus Left-Thalamus basal ganglia
5 left Thalamus Proper Left-Thalamus basal ganglia
6 left Thalamus Proper Left-Thalamus basal ganglia
7 left Caudate Left-Caudate basal ganglia
8 left Caudate Left-Caudate basal ganglia
9 left Putamen Left-Putamen basal ganglia
10 left Putamen Left-Putamen basal ganglia
Message
... with 37 more rows
print.ggseg_atlas rendering branches / prints a cortical atlas (vertices)
Code
print(dk())
Message
-- dk ggseg atlas --------------------------------------------------------------
Type: cortical
Regions: 35
Hemispheres: left, right
Views: inferior, lateral, superior, medial
Palette: v
Rendering: v ggseg
v ggseg3d (vertices)
--------------------------------------------------------------------------------
Output
hemi region label
1 left banks of superior temporal sulcus lh_bankssts
2 left caudal anterior cingulate lh_caudalanteriorcingulate
3 left caudal middle frontal lh_caudalmiddlefrontal
4 left corpus callosum lh_corpuscallosum
5 left cuneus lh_cuneus
6 left entorhinal lh_entorhinal
7 left fusiform lh_fusiform
8 left inferior parietal lh_inferiorparietal
9 left inferior temporal lh_inferiortemporal
10 left isthmus cingulate lh_isthmuscingulate
lobe
1 temporal
2 cingulate
3 frontal
4 white matter
5 occipital
6 temporal
7 temporal
8 parietal
9 temporal
10 cingulate
Message
... with 60 more rows
print.ggseg_atlas rendering branches / prints an atlas with no 3D geometry as none
Code
print(atlas)
Message
-- test ggseg atlas ------------------------------------------------------------
Type: cerebellar
Regions: 1
Hemispheres: left
Views: lateral
Palette: x
Rendering: v ggseg
x ggseg3d (none)
--------------------------------------------------------------------------------
Output
hemi region label
1 left frontal lh_frontal
print.ggseg_atlas rendering branches / prints a polygon atlas summary with views
Code
print(poly_atlas)
Message
-- dk ggseg atlas --------------------------------------------------------------
Type: cortical
Regions: 35
Hemispheres: left, right
Views: inferior, lateral, superior, medial
Palette: v
Rendering: v ggseg
v ggseg3d (vertices)
--------------------------------------------------------------------------------
Output
hemi region label
1 left banks of superior temporal sulcus lh_bankssts
2 left caudal anterior cingulate lh_caudalanteriorcingulate
3 left caudal middle frontal lh_caudalmiddlefrontal
4 left corpus callosum lh_corpuscallosum
5 left cuneus lh_cuneus
6 left entorhinal lh_entorhinal
7 left fusiform lh_fusiform
8 left inferior parietal lh_inferiorparietal
9 left inferior temporal lh_inferiortemporal
10 left isthmus cingulate lh_isthmuscingulate
lobe
1 temporal
2 cingulate
3 frontal
4 white matter
5 occipital
6 temporal
7 temporal
8 parietal
9 temporal
10 cingulate
Message
... with 60 more rows
Try the ggseg.formats package in your browser
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