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Copy pathWHS_SD_Rat_v3_39um.json
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WHS_SD_Rat_v3_39um.json
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{"name":"WHS SD Rat v3","encoding":1,"xdim":512,"ydim":1024,"zdim":512,"labels":[{},
{"rgb":"ff3427","name":"descending corticofugal pathways"},
{"rgb":"ffba00","name":"substantia nigra"},
{"rgb":"0000ff","name":"subthalamic nucleus"},
{"rgb":"ffff00","name":"molecular layer of the cerebellum"},
{"rgb":"00ffff","name":"granule cell level of the cerebellum"},
{"rgb":"ff00ff","name":"alveus of the hippocampus"},
{"rgb":"34ff0d","name":"inferior cerebellar peduncle"},
{"rgb":"1d68eb","name":"cingulate cortex, area 2"},
{"rgb":"814fff","name":"striatum"},
{"rgb":"ff91ba","name":"globus pallidus"},
{"rgb":"1ae7ff","name":"entopeduncular nucleus"},
{"rgb":"022cff","name":"ventricular system"},
{"rgb":"d4ff00","name":"medial lemniscus"},
{"rgb":"ff19f0","name":"facial nerve"},
{"rgb":"7cfc00","name":"anterior commissure, anterior part"},
{"rgb":"ffba00","name":"anterior commissure, posterior part"},
{"rgb":"ae00e8","name":"ventral hippocampal commissure"},
{"rgb":"006400","name":"thalamus"},
{"rgb":"ff0800","name":"septal region"},
{"rgb":"30da00","name":"optic nerve"},
{"rgb":"267eff","name":"optic tract and optic chiasm"},
{"rgb":"daaa3e","name":"pineal gland"},
{"rgb":"86ff5a","name":"spinal cord"},
{"rgb":"21e6ff","name":"commissure of the superior colliculus"},
{"rgb":"9953ff","name":"brainstem"},
{"rgb":"e278a1","name":"hypothalamic region"},
{"rgb":"5600dd","name":"superficial gray layer of the superior colliculus"},
{"rgb":"07ff59","name":"periaqueductal gray"},
{"rgb":"15c0ff","name":"fornix"},
{"rgb":"eeba00","name":"mammillothalamic tract"},
{"rgb":"adff2f","name":"commissural stria terminalis"},
{"rgb":"e1970f","name":"deeper layers of the superior colliculus"},
{"rgb":"eb57ff","name":"periventricular gray"},
{"rgb":"faf4f7","name":"genu of the facial nerve"},
{"rgb":"00d70b","name":"pontine nuclei"},
{"rgb":"00ff1d","name":"fimbria of the hippocampus"},
{"rgb":"f44345","name":"fasciculus retroflexus"},
{"rgb":"00ff00","name":"stria medullaris of the thalamus"},
{"rgb":"ee7533","name":"stria terminalis"},
{"rgb":"ff00da","name":"posterior commissure"},
{"rgb":"0f6de6","name":"glomerular layer of the accessory olfactory bulb"},
{"rgb":"ffe300","name":"glomerular layer of the olfactory bulb"},
{"rgb":"ff8700","name":"olfactory bulb"},
{"rgb":"ff6e00","name":"corpus callosum and associated subcortical white matter"},
{"rgb":"bc20ad","name":"brachium of the superior colliculus"},
{"rgb":"ff2a27","name":"inferior colliculus, commissure"},
{"rgb":"27f4fd","name":"central canal"},
{"rgb":"3fc0ff","name":"interpeduncular nucleus"},
{"rgb":"b31c35","name":"ascending fibers of the facial nerve"},
{"rgb":"ff4fce","name":"anterior commissure"},
{"rgb":"00f60e","name":"inferior olive"},
{"rgb":"5bf1ff","name":"spinal trigeminal nucleus"},
{"rgb":"fa8072","name":"spinal trigeminal tract"},
{"rgb":"ced307","name":"frontal association cortex"},
{"rgb":"86cc4c","name":"middle cerebellar peduncle"},
{"rgb":"80aaff","name":"transverse fibers of the pons"},
{"rgb":"45ebca","name":"habenular commissure"},
{"rgb":"de07ed","name":"nucleus of the stria medullaris"},
{"rgb":"e1f00d","name":"basal forebrain region"},
{"rgb":"faaa40","name":"supraoptic decussation"},
{"rgb":"4196ff","name":"medial lemniscus decussation"},
{"rgb":"7209d4","name":"pyramidal decussation"},
{"rgb":"03c12d","name":"neocortex"},
{"rgb":"0008b6","name":"bed nucleus of the stria terminalis"},
{"rgb":"ff571e","name":"pretectal region"},
{"rgb":"a5836b","name":"cornu ammonis 3"},
{"rgb":"5b2d0a","name":"dentate gyrus"},
{"rgb":"ffff00","name":"cornu ammonis 2"},
{"rgb":"d9680d","name":"cornu ammonis 1"},
{"rgb":"ff0000","name":"fasciola cinereum"},
{"rgb":"ffc000","name":"subiculum"},
{"rgb":"287082","name":"postrhinal cortex"},
{"rgb":"507baf","name":"presubiculum"},
{"rgb":"173660","name":"parasubiculum"},
{"rgb":"cd33ff","name":"perirhinal area 35"},
{"rgb":"7030a0","name":"perirhinal area 36"},
{"rgb":"7abb33","name":"entorhinal cortex"},
{"rgb":"5a6f2f","name":"lateral entorhinal cortex"},
{"rgb":"009037","name":"vestibular apparatus"},
{"rgb":"00ff1d","name":"cochlea"},
{"rgb":"fd9400","name":"cochlear nerve"},
{"rgb":"fd3200","name":"vestibular nerve"},
{"rgb":"000cff","name":"ventral cochlear nucleus, granule cell layer"},
{"rgb":"341d90","name":"4th ventricle"},
{"rgb":"5c9cd3","name":"dorsal cochlear nucleus, molecular layer"},
{"rgb":"00509c","name":"dorsal cochlear nucleus, fusiform and granule layer"},
{"rgb":"c5eeff","name":"dorsal cochlear nucleus, deep core"},
{"rgb":"ffd900","name":"acoustic striae"},
{"rgb":"d5ff00","name":"trapezoid body"},
{"rgb":"00ff51","name":"nucleus of the trapezoid body"},
{"rgb":"00eeff","name":"superior paraolivary nucleus"},
{"rgb":"dbef3d","name":"medial superior olive"},
{"rgb":"234cbe","name":"lateral superior olive"},
{"rgb":"019915","name":"superior periolivary region"},
{"rgb":"00aeff","name":"ventral periolivary nuclei"},
{"rgb":"ff0073","name":"lateral lemniscus, ventral nucleus"},
{"rgb":"ab105b","name":"lateral lemniscus, intermediate nucleus"},
{"rgb":"6c125b","name":"lateral lemniscus, dorsal nucleus"},
{"rgb":"ff1d00","name":"lateral lemniscus, commissure"},
{"rgb":"ffa600","name":"lateral lemniscus"},
{"rgb":"ceff8e","name":"inferior colliculus, dorsal cortex"},
{"rgb":"00eeff","name":"inferior colliculus, central nucleus"},
{"rgb":"3088cb","name":"inferior colliculus, external cortex"},
{"rgb":"b03a48","name":"inferior colliculus, brachium"},
{"rgb":"0af4d9","name":"medial geniculate body, medial division"},
{"rgb":"efa300","name":"medial geniculate body, dorsal division"},
{"rgb":"833a1f","name":"medial geniculate body, ventral division"},
{"rgb":"ff2ff2","name":"medial geniculate body, marginal zone"},
{"rgb":"ffd700","name":"primary auditory cortex"},
{"rgb":"f0ffff","name":"secondary auditory cortex, dorsal area"},
{"rgb":"d8bfd8","name":"secondary auditory cortex, ventral area"},
{"rgb":"f49cff","name":"auditory radiation"},
{"rgb":"2298ff","name":"ventral cochlear nucleus, anterior part"},
{"rgb":"00e6cf","name":"ventral cochlear nucleus, posterior part"},
{"rgb":"00ff6a","name":"ventral cochlear nucleus, cap area"},
{"rgb":"b9ffe9","name":"spiral ganglion"},
{"rgb":"63cd00","name":"nucleus sagulum"},
{"rgb":"6e00ff","name":"reticular thalamic nucleus, auditory segment"}],
"transformations":[
{"name":"WHS [mm] RAS","matrix":[[0.0390625,0,0,0],[0,0.0390625,0,0],[0,0,0.0390625,0],[-9.53125,-24.335938,-9.6875,1]]},
{"name":"WHS [voxel] RAS","matrix":[[1,0,0,0],[0,1,0,0],[0,0,1,0],[-244,-623,-248,1]]},
{"name":"Stereotaxic [mm] Bregma RPI","matrix":[[0.039051742,-0.000367872,0.000839666,0],[-0.000270531,-0.038810515,-0.004421499,0],[0.000875889,0.004414466,-0.038802374,0],[-9.815462651,23.49139767,19.75372551,1]]},
{"name":"Stereotaxic [mm] Interaural midpoint RPI","matrix":[[0.039051742,-0.000367872,0.000839666,0],[-0.000270531,-0.038810515,-0.004421499,0],[0.000875889,0.004414466,-0.038802374,0],[-9.815462651,14.43114894,14.3031771,1]]}
],
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