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XeniosPXeniosP
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added initial rat atlas
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5 files changed

+278
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‎js/coreweb/bisweb_apputilities.js‎

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@@ -61,6 +61,15 @@ module.exports = {
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callback(`${imagepath}/Symmetric_N162_0.10.nii.gz`,viewerno,'LPS');
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});
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}
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if (species==='all' || species==='rat') {
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webutil.createMenuItem(fmenu,'Load Sigma Rat Template (0.15mm, RAS)',
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function() {
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let imagepath=webutil.getWebPageImagePath();
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callback(`${imagepath}/SIGMA_stripped_rat_mri.nii.gz`,viewerno,'RAS');
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}
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)
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}
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resolve();
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}).catch( (e) => {
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reject(e);
@@ -106,6 +115,15 @@ module.exports = {
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callback(`${imagepath}/N162_yaleallen_010.nii.gz`,viewerno,'LPS');
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});
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}
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if (species==='all' || species==='rat') {
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webutil.createMenuItem(fmenu,'Load Sigma-Yale Regions (0.15mm, RAS)',
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function() {
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let imagepath=webutil.getWebPageImagePath();
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callback(`${imagepath}/SIGMA_Invivo_atlas_regions.nii.gz`,viewerno,'RAS');
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});
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}
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resolve();
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}).catch( (e) => {
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reject(e);

‎web/images/SIGMA_Invivo_atlas_regions.nii.gz‎

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‎web/images/SIGMA_stripped_rat_mri.nii.gz‎

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‎web/images/atlases/atlaslist.json‎

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"ismni" : false,
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"correctstr" : "Must be RAS 118x90x160 (or 117x90x160) and 0.1x0.1x0.1 mm",
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"multiressurfaces" : false
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},
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"sigmarat" : {
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"name" : "sigmarat",
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"filename" : "sigmarat.json",
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"dimensions" : [ 128,218,128 ],
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"spacing" : [ 0.15,0.15,0.15 ],
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"midlobe" : 100,
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"halflobe" : 50,
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"origin" : [ 63,96,63 ],
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"midoffset" : 5.0,
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"axisoffset" : [0,5.0,20.0],
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"axissize" : [ 127.0,217.0, 127.0 ],
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"ismni" : false,
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"correctstr" : "Must be RAS 128x218x128 and 0.15x0.15x0.15 mm",
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"multiressurfaces" : false
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}
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}

‎web/images/atlases/sigmarat.json‎

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{
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"anatomical": "SIGMA_stripped_rat_mri.nii.gz",
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"species": "rat",
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"labels": {
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"filename": "SIGMA_Invivo_atlas_regions.nii.gz",
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"description": "SIGMA Regions",
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"extra": "Rat Brain",
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"data": [
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{
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"name": "Sigma Rat Regions",
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"description": "Regions as defined by Sigma atlas",
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"labels": {
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"1" : "corticofugal tract and corona radiata",
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"3" : "Subthalamic nucleus",
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"4" : "Molecular cell layer of the cerebellum",
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"5" : "Cerebellum, unspecified",
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"6" : "alveus of the hippocampus",
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"7" : "inferior cerebellar peduncle",
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"10" : "Cingulate area 2",
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"32" : "Entopeduncular nucleus",
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"33" : "Ventricular system, unspecified",
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"34" : "medial lemniscus, unspecified",
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"35" : "facial nerve, unspecified",
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"36" : "anterior commissure, anterior limb",
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"37" : "anterior commissure, posterior limb",
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"38" : "ventral hippocampal commissure",
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"40" : "Septal region",
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"41" : "optic nerve",
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"42" : "optic tract and optic chiasm",
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"43" : "Pineal gland",
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"45" : "Spinal cord",
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"46" : "commissure of the superior colliculus",
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"47" : "Brainstem, unspecified",
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"48" : "Hypothalamic region, unspecified",
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"50" : "Superficial gray layer of the superior colliculus",
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"51" : "Periaqueductal gray",
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"52" : "fornix",
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"53" : "mammillotegmental tract",
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"54" : "commissural stria terminalis",
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"55" : "Deeper layers of the superior colliculus",
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"56" : "Periventricular gray",
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"57" : "genu of the facial nerve",
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"58" : "Pontine nuclei",
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"59" : "fimbria of the hippocampus",
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"60" : "fasciculus retroflexus",
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"61" : "stria medullaris thalami",
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"62" : "stria terminalis",
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"63" : "posterior commissure",
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"64" : "Glomerular layer of the accessory olfactory bulb",
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"65" : "Glomerular layer of the olfactory bulb",
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"66" : "Olfactory bulb, unspecified",
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"67" : "corpus callosum and associated subcortical white matter",
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"68" : "brachium of the superior colliculus",
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"69" : "inferior colliculus, commissure",
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"70" : "Central canal",
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"71" : "Interpeduncular nucleus",
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"72" : "ascending fibers of the facial nerve",
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"73" : "anterior commissure, intrabulbar part",
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"74" : "Inferior olive",
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"75" : "Spinal trigeminal nucleus",
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"76" : "spinal trigeminal tract",
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"77" : "Frontal association cortex",
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"78" : "middle cerebellar peduncle",
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"79" : "transverse fibers of the pons",
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"80" : "habenular commissure",
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"81" : "Nucleus of the stria medullaris",
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"82" : "Basal forebrain region, unspecified",
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"83" : "supraoptic decussation",
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"84" : "medial lemniscus decussation",
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"85" : "pyramidal decussation",
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"93" : "Bed nucleus of the stria terminalis",
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"94" : "Pretectal region",
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"95" : "Cornu ammonis 3",
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"96" : "Dentate gyrus",
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"97" : "Cornu ammonis 2",
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"98" : "Cornu ammonis 1",
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"99" : "Fasciola cinereum",
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"100" : "Subiculum",
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"108" : "Postrhinal cortex",
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"109" : "Presubiculum",
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"110" : "Parasubiculum",
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"112" : "Perirhinal area 35",
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"113" : "Perirhinal area 36",
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"114" : "Medial entorhinal cortex",
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"115" : "Lateral entorhinal cortex",
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"119" : "Vestibular apparatus",
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"120" : "Cochlea",
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"121" : "Cochlear nerve",
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"122" : "Vestibular nerve",
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"123" : "Ventral cochlear nucleus, granule cell layer",
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"125" : "4th ventricle",
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"126" : "Dorsal cochlear nucleus, molecular layer",
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"127" : "Dorsal cochlear nucleus, fusiform and granule layer",
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"128" : "Dorsal cochlear nucleus, deep core",
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"129" : "acoustic striae",
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"130" : "trapezoid body",
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"131" : "Nucleus of the trapezoid body",
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"132" : "Superior paraolivary nucleus",
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"133" : "Medial superior olive",
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"134" : "Lateral superior olive",
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"135" : "Superior periolivary region",
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"136" : "Ventral periolivary nuclei",
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"137" : "Lateral lemniscus, ventral nucleus",
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"138" : "Lateral lemniscus, intermediate nucleus",
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"139" : "Lateral lemniscus, dorsal nucleus",
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"140" : "lateral lemniscus, commissure",
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"141" : "lateral lemniscus, unspecified",
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"142" : "Inferior colliculus, dorsal cortex",
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"143" : "Inferior colliculus, central nucleus",
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"145" : "Inferior colliculus, external cortex",
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"146" : "inferior colliculus, brachium",
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"150" : "Medial geniculate body, marginal zone",
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"151" : "Primary auditory area",
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"152" : "Secondary auditory area, dorsal part",
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"153" : "Secondary auditory area, ventral part",
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"157" : "external medullary lamina, auditory radiation",
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"158" : "Ventral cochlear nucleus, anterior part",
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"159" : "Ventral cochlear nucleus, posterior part",
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"160" : "Ventral cochlear nucleus, cap area",
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"162" : "Spiral ganglion",
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"163" : "Nucleus sagulum",
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"164" : "Reticular (pre)thalamic nucleus, auditory segment",
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"180" : "lateral olfactory tract",
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"181" : "Piriform cortex, layer 1",
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"182" : "Piriform cortex, layer 2",
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"183" : "Piriform cortex, layer 3",
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"184" : "Nucleus accumbens, core",
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"187" : "Substantia nigra, reticular part",
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"188" : "Substantia nigra, compact part",
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"189" : "Substantia nigra, lateral part",
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"192" : "Nucleus accumbens, shell",
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"193" : "Ventral pallidum",
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"195" : "Globus pallidus external, medial part",
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"196" : "Ventral tegmental area",
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"197" : "Caudate putamen",
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"198" : "Globus pallidus external, lateral part",
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"199" : "Ventral striatal region, unspecified",
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"200" : "Reticular (pre)thalamic nucleus, unspecified",
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"201" : "Peripeduncular nucleus",
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"204" : "Pregeniculate nucleus",
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"205" : "Dorsal lateral geniculate nucleus",
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"206" : "Lateral habenular nucleus",
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"207" : "Medial habenular nucleus",
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"208" : "Posterior intralaminar nucleus",
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"210" : "Posterior thalamic nuclear group, triangular part",
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"211" : "Parataenial thalamic nucleus",
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"213" : "Anterodorsal thalamic nucleus",
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"214" : "Anteroventral thalamic nucleus, dorsomedial part",
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"215" : "Anteroventral thalamic nucleus, ventrolateral part",
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"216" : "Rhomboid thalamic nucleus",
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"218" : "Xiphoid thalamic nucleus",
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"219" : "Reuniens thalamic nucleus",
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"221" : "Ventromedial thalamic nucleus",
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"222" : "Submedius thalamic nucleus",
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"223" : "Angular thalamic nucleus",
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"227" : "Ventral posteromedial thalamic nucleus",
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"228" : "Laterodorsal thalamic nucleus, dorsomedial part",
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"229" : "Laterodorsal thalamic nucleus, ventrolateral part",
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"230" : "Posterior thalamic nucleus",
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"231" : "Ventrolateral thalamic nucleus",
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"232" : "Mediodorsal thalamic nucleus, lateral part",
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"233" : "Mediodorsal thalamic nucleus, central part",
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"235" : "Zona incerta, dorsal part",
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"236" : "Zona incerta, ventral part",
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"238" : "Zona incerta, A13 dopamine cells",
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"239" : "pretectothalamic lamina",
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"240" : "Mediodorsal thalamic nucleus, medial part",
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"242" : "Paraventricular thalamic nuclei (anterior and posterior)",
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"246" : "Paracentral thalamic nucleus",
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"247" : "Central medial thalamic nucleus",
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"248" : "Central lateral thalamic nucleus",
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"249" : "external medullary lamina, unspecified",
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"254" : "Anteromedial thalamic nucleus",
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"255" : "Interanteromedial thalamic nucleus",
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"257" : "Zona incerta, rostral part",
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"260" : "Intermediodorsal thalamic nucleus",
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"266" : "Ventral posterior nucleus of the thalamus, parvicellular part",
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"267" : "Parafascicular thalamic nucleus",
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"268" : "Retroreuniens thalamic nucleus",
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"270" : "superior cerebellar peduncle and prerubral field",
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"272" : "Intergeniculate leaflet",
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"278" : "Subparafascicular nucleus",
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"280" : "Fields of Forel",
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"281" : "Subgeniculate nucleus",
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"282" : "Ethmoid-Limitans nucleus",
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"283" : "Lateral posterior thalamic nucleus, lateral part",
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"284" : "Zona incerta, A11 dopamine cells",
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"285" : "Lateral posterior thalamic nucleus, mediorostral part",
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"286" : "Lateral posterior thalamic nucleus, mediocaudal part",
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"287" : "Zona incerta, caudal part",
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"290" : "intramedullary thalamic area",
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"291" : "internal medullary lamina",
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"293" : "Ventral anterior thalamic nucleus",
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"294" : "Ventral posterolateral thalamic nucleus",
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"295" : "Medial geniculate body, dorsal division",
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"297" : "Medial geniculate body, medial division",
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"298" : "Medial geniculate body, ventral division",
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"299" : "Medial geniculate body, suprageniculate nucleus",
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"400" : "Ventrolateral orbital area",
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"401" : "Lateral orbital area",
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"402" : "Ventral orbital area",
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"403" : "Medial orbital area",
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"404" : "Dorsolateral orbital area",
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"405" : "Prelimbic area",
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"406" : "Secondary motor area",
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"407" : "Frontal association area 3",
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"408" : "Primary motor area",
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"409" : "Agranular insular cortex, ventral area",
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"410" : "Agranular insular cortex dorsal area ",
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"411" : "Cingulate area 1",
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"412" : "Claustrum",
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"413" : "Infralimbic area",
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"414" : "Dysgranular insular cortex",
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"416" : "Granular insular cortex",
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"417" : "Primary somatosensory area, forelimb representation",
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"418" : "Primary somatosensory area, dysgranular zone",
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"420" : "Primary somatosensory area, face representation",
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"422" : "Secondary somatosensory area",
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"423" : "Primary somatosensory area, hindlimb representation",
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"424" : "Agranular insular cortex, posterior area ",
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"425" : "Primary somatosensory area, barrel field",
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"427" : "Retrosplenial dysgranular area",
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"429" : "Primary somatosensory area, trunk representation",
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"430" : "Retrosplenial granular area",
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"432" : "Parietal association cortex, lateral area",
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"433" : "Parietal association cortex, medial area",
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"436" : "Parietal association cortex, posterior area ",
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"442" : "Primary visual area",
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"443" : "Secondary visual area, lateral part",
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"444" : "Temporal association cortex",
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"448" : "Secondary visual area, medial part",
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"500" : "Endopiriform nucleus",
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"501" : "Amygdaloid area, unspecified",
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"502" : "Nucleus of the lateral olfactory tract"
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}
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}
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]
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},
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"parcellations": [ ],
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"groupdefinitions": [
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{
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"lobes": 0
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}
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]
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}

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