Table 1.
Subcortical Atlas of the Marmoset (“SAM”)—Version 1.0
| Atlas label # | Abbreviations | Basal ganglia subregions and associated fiber bundles and Claustrum | |
| 1 | pu | Putamen | Striatum |
| 2 | cd | Caudate nucleus | Striatum |
| 3 | NA | Nucleus accumbens | Ventral striatum |
| 210 | OT | Olfactory tubercle | Ventral striatum |
| 10 | VP | Ventral pallidum | Pallidum |
| 4 | GPe | Globus pallidus external segment | Pallidum |
| 5 | GPi | Globus pallidus internal segment | Pallidum |
| 9 | STN | Subthalamic nucleus | Nigral region |
| 6 | SNpr | Substantia nigra pars reticulata | Nigral region |
| 7 | SNpc | Substantia nigra pars compacta | Nigral region |
| 8 | SNpl | Substantia nigra pars lateralis | Nigral region |
| 70 | SNpm | Substantia nigra pars mixta | Nigral region |
| 215 | lf_al | Lenticular fasciculus and ansa lenticularis | Fiber bundle |
| 213 | H1 | H1 field of Forel | Fiber bundle |
| 212 | H2 | H2 field of Forel | Fiber bundle |
| 211 | mb | Muratoff bundle | Fiber bundle |
| 66 | ac | Anterior commissure | Fiber bundle |
| 474 | cla | Claustrum | other subcortical region |
| Red nucleus | |||
| 526 | prf | Prerubral field | Brainstem/Midbrain |
| 41 | RNpc | Red nucleus, parvicellular division | Brainstem/Midbrain |
| 122 | RNmc | Red nucleus, magnocellular division | Brainstem/Midbrain |
| Thalamic subregions and associated fiber bundles | |||
| 11 | AV | Anterior ventral nucleus | Dorsal thalamus_anterior group |
| 12 | AM | Anterior medial nucleus | Dorsal thalamus_anterior group |
| 128 | AD | Anterior dorsal nucleus | Dorsal thalamus_anterior group |
| 15 | LD | Lateral dorsal nucleus | Dorsal thalamus_anterior group |
| 13 | VApc | Ventral anterior nucleus, parvicellular division | Dorsal thalamus_lateral group |
| 14 | VAmc | Ventral anterior nucleus, magnocellular division | Dorsal thalamus_lateral group |
| 19 | VLc | Ventral lateral caudal nucleus | Dorsal thalamus_lateral group |
| 20 | VLo | Ventral lateral oral nucleus | Dorsal thalamus_lateral group |
| 21 | VPI | Ventral posterior inferior nucleus | Dorsal thalamus_lateral group |
| 22 | VPM | Ventral posterior medial nucleus | Dorsal thalamus_lateral group |
| 23 | VPMpc | Ventral posterior medial nucleus, parvicellular division | Dorsal thalamus_lateral group |
| 26 | LP | Lateral posterior nucleus | Dorsal thalamus_lateral group |
| 27 | VPLc | Ventral posterior lateral caudal nucleus | Dorsal thalamus_lateral group |
| 103 | VLps | Ventral lateral postrema nucleus | Dorsal thalamus_lateral group |
| 127 | pt | Parataenial nucleus | Dorsal thalamus_medial group |
| 38 | Pa | Paraventricular nucleus | Dorsal thalamus_medial group |
| 16 | MDmc | Mediodorsal nucleus, magnocellular division | Dorsal thalamus_medial group |
| 17 | MDpc | Mediodorsal nucleus, parvicellular division | Dorsal thalamus_medial group |
| 18 | MDmf | Mediodorsal nucleus, multiform division | Dorsal thalamus_medial group |
| 31 | MDdc | Mediodorsal nucleus, densocellular division | Dorsal thalamus_medial group |
| 228 | cif | Central inferior nucleus | Dorsal thalamus_medial group |
| 229 | cdc | Central dorsocellular nucleus | Dorsal thalamus_medial group |
| 131 | Re | Reunions nucleus | Dorsal thalamus_medial group |
| 106 | cim | Central intermediate nucleus | Dorsal thalamus_medial group |
| 24 | cnMD | Centromedian nucleus | Dorsal thalamus_intralaminar group |
| 25 | Pf | Parafascicular nucleus | Dorsal thalamus_intralaminar group |
| 104 | csl | Central superior lateral nucleus | Dorsal thalamus_intralaminar group |
| 105 | cl | Central lateral nucleus | Dorsal thalamus_intralaminar group |
| 129 | pcn | Paracentral nucleus | Dorsal thalamus_intralaminar group |
| 130 | clc | Central latocellular nucleus | Dorsal thalamus_intralaminar group |
| 28 | PM | Medial pulvinar | Dorsal thalamus_posterior group |
| 29 | PL | Lateral pulvinar | Dorsal thalamus_posterior group |
| 523 | PIc | Inferior pulvinar, central nucleus | Dorsal thalamus_posterior group |
| 524 | PIm | Inferior pulvinar, medial nucleus | Dorsal thalamus_posterior group |
| 525 | PIp | Inferior pulvinar, posterior nucleus | Dorsal thalamus_posterior group |
| 132 | Pulo | Pulvinar oralis nucleus | Dorsal thalamus_posterior group |
| 135 | ptg | Posterior thalamic group | Dorsal thalamus_posterior group |
| 32 | LGN | Lateral geniculate nucleus | Geniculate region |
| 510 | MGv | Medial geniculate nucleus, ventral division | Geniculate region |
| 511 | MGad | Medial geniculate nucleus, anterodorsal division | Geniculate region |
| 512 | MGm | Medial geniculate nucleus, medial division | Geniculate region |
| 513 | MGz | Medial geniculate nucleus, transition zone | Geniculate region |
| 514 | MGpd | Medial geniculate nucleus, posterodorsal division | Geniculate region |
| 34 | Hl | Lateral habenular nucleus | Epithalamus |
| 35 | Hm | Medial habenular nucleus | Epithalamus |
| 136 | Sg | Suprageniculate nucleus | Other thalamic region |
| 36 | r | Reticular nucleus | Other thalamic region |
| 37 | zic | Zona incerta | Other thalamic region |
| 126 | Sm | Stria medullaris | Fiber bundle |
| 175 | iml | Internal medullary lamina | Fiber bundle |
| Hypothalamic subregions and associated fiber bundles | |||
| 160 | POA | Preoptic area | anterior group |
| 161 | PVN | Paraventricular nucleus | anterior group |
| 162 | SON | Supraoptic nucleus | anterior group |
| 163 | SCN | Suprachiasmatic nucleus | anterior group |
| 164 | DM | Dorsomedial hypothalamic nucleus | Middle (Tuberal and medial) group |
| 165 | VM | Ventromedial hypothalamic nucleus | Middle (Tuberal and medial) group |
| 166 | LT | Lateral hypothalamic nucleus | Middle (Tuberal and medial) group |
| 167 | Arh | Arcuate hypothalamic nucleus | Middle (Tuberal and medial) group |
| 168 | SOR | Supraoptic nucleus, retrochiasmatic part | Middle (Tuberal and medial) group |
| 243 | mtn | Medial tuberal nucleus | Middle (Tuberal and medial) group |
| 193 | TCA | Tuber cinereum area | Middle (Tuberal and medial) group |
| 243 | mtn | Medial tuberal nucleus | Middle (Tuberal and medial) group |
| 170 | PMN | Paramammillary nucleus | Posterior group |
| 39 | MMN | Medial mammillary nucleus | Posterior group |
| 40 | LMN | Lateral mammillary nucleus | Posterior group |
| 191 | SMN | Supramammillary nucleus | Posterior group |
| 67 | OC | Optic chiasm | Fiber bundle |
| 68 | ot | Optic tract | Fiber bundle |
| Brainstem (Midbrain, Pons, and Medulla)/Spinal cord junction and associated fiber bundles | |||
| 42 | 3rd | Third cranial (oculomotor) nuclei | Midbrain |
| 43 | 4th | Fourth cranial (trochlear) nuclei | Midbrain |
| 44 | SC | Superior colliculus | Midbrain |
| 45 | IC | Inferior colliculus | Midbrain |
| 226 | DR | Dorsal raphe | Midbrain |
| 227 | DTg | Dorsal tegmental nucleus | Midbrain |
| 133 | PAG | Periaqueductal gray | Midbrain |
| 138 | inc | Interstitial nucleus of Cajal | Midbrain |
| 139 | nd | Nucleus of Darkschewitsch | Midbrain |
| 140 | IPN | Interpeduncular nucleus | Midbrain |
| 142 | VTA | Ventral tegmental area | Midbrain |
| 159 | PN | Pontine nuclei | Midbrain |
| 177 | MR | Median raphe | Midbrain |
| 180 | vnll | Ventral nucleus of lateral lemniscus | Midbrain |
| 181 | dnll | Dorsal nucleus of lateral lemniscus | Midbrain |
| 268 | APN | Anterior pretectal nucleus | Midbrain |
| 269 | MRF | Midbrain reticular formation | Midbrain |
| 183 | nbic | Nucleus of brachium of inferior colliculus | Midbrain |
| 184 | pbgn | Parabigeminal nucleus | Midbrain |
| 189 | ldtn | Lateral dorsal tegmental nucleus | Midbrain |
| 273 | ltn | Lateral terminal nucleus | Midbrain |
| 274 | atn | Anterior tegmental nucleus | Midbrain |
| 275 | San | Sagulum nucleus | Midbrain/Pons |
| 276 | PRF | Pontine reticular formation | Midbrain/Pons |
| 46 | 5th | Fifth cranial (trigeminal) nuclei | Pons |
| 47 | 6th | Sixth cranial (abducent) nuclei | Pons |
| 48 | 7th | Seventh cranial (facial) nuclei | Pons |
| 52 | soc | Superior olivary complex | Pons |
| 218 | lc | Locus coeruleus | Pons |
| 220 | MC5_nu | Mesencephalic trigeminal nucleus | Pons |
| 221 | PBN | Parabrachial nucleus | Pons |
| 251 | sVN | Superior vestibular nucleus | Pons |
| 252 | pstn | Principal sensory trigeminal nucleus | Pons |
| 254 | RF (ngc) | Reticular formation, nucleus gigantocellularis | Pons |
| 257 | nro | Nucleus raphe obscurus | Pons |
| 258 | nrm | Nucleus raphe magnus | Pons |
| 259 | nrp | Nucleus raphe pallidus | Pons |
| 260 | RF (npo) | Reticular formation, nucleus pontis centralis oralis | Pons |
| 270 | dpgn | Dorsal paragigantocellular nucleus | Pons |
| 271 | lpgn | Lateral paragigantocellular nucleus | Pons |
| 272 | nrip | Nucleus raphe interpositus | Pons |
| 267 | rtn | Reticulo-tegmental nucleus | Pons |
| 528 | ntb | Nucleus of trapezoid body | Pons |
| 50 | stn | Spinal trigeminal nucleus | pons and medulla |
| 248 | mVN | Medial vestibular nucleus | Pons and medulla |
| 249 | lVN | Lateral vestibular nucleus | Pons and medulla |
| 250 | spVN | Spinal vestibular nucleus | Pons and medulla |
| 51 | ion | Inferior olivary nucleus | Medulla |
| 53 | chn | Cochlear nucleus | Medulla |
| 54 | 12th | Twelfth cranial (hypoglossal) nuclei | Medulla |
| 55 | denv_10 | Dorsal motor nucleus of vagus (tenth cranial nuclei) | Medulla |
| 56 | sn | Solitary nucleus | Medulla |
| 57 | np | Nucleus prepositus | Medulla |
| 230 | AN | Ambiguus nucleus | Medulla |
| 58 | gn | Gracile nucleus | Medulla |
| 59 | cn | Cuneate nucleus | Medulla |
| 60 | lcn | Lateral cuneate nucleus | Medulla |
| 232 | lrn | Lateral reticular nucleus | Medulla |
| 255 | irn | Intermediate reticular nucleus | Medulla |
| 256 | prn | Parvicellular reticular nucleus | Medulla |
| 261 | mrn_d | Medullary reticular nucleus, dorsal part | Medulla |
| 262 | mrn_v | Medullary reticular nucleus, ventral part | Medulla |
| 265 | stn (g) | Spinal trigeminal nucleus, gelatinosa layer | Spinal cord |
| 266 | IX-lamina 9 | Lamina 9 of the spinal gray | Spinal cord |
| 278 | CG | Central gray | Spinal cord |
| 134 | bsc | Brachium of superior colliculus | Fiber bundle |
| 144 | mlf | Medial longitudinal fasciculus | Fiber bundle |
| 145 | SCPX | Superior cerebellar peduncle decussation | Fiber bundle |
| 147 | gf | Gracile fasciculus | Fiber bundle |
| 148 | ml | Medial lemniscus | Fiber bundle |
| 149 | tb | Trapezoid body | Fiber bundle |
| 152 | cf | Cuneate fasciculus | Fiber bundle |
| 153 | SCP | Superior cerebellar peduncle | Fiber bundle |
| 154 | pc | Posterior commissure | Fiber bundle |
| 157 | ic_CP_CST_CBT | Internal capsule, cerebral peduncle, corticospinal, or corticobulbar tract | Fiber bundle |
| 182 | bic | Brachium of inferior colliculus | Fiber bundle |
| 185 | ll | Lateral lemniscus | Fiber bundle |
| 190 | MTT | Mammillothalamic tract | Fiber bundle |
| 216 | ICP | Inferior cerebellar peduncle | Fiber bundle |
| 217 | MCP | Middle cerebellar peduncle | Fiber bundle |
| 219 | MC5_t | Mesencephalic trigeminal tract | Fiber bundle |
| 263 | LCST | Lateral corticospinal tract | Fiber bundle |
| 277 | ACST | Anterior corticospinal tract | Fiber bundle |
| 264 | pd | Pyramidal decussation | Fiber bundle |
| 527 | 5n | Motor root of trigeminal nerve | Fiber bundle |
| 529 | 7n | Facial nerve | Fiber bundle |
| 530 | fc | Facial colliculus | Fiber bundle |
| 531 | st | Solitary tract | Fiber bundle |
| 244 | vsct | Ventral spinocerebellar tract | Fiber bundle |
| 245 | cic | Commissure of inferior colliculus | Fiber bundle |
| 246 | csc | Commissure of superior colliculus | Fiber bundle |
| 247 | oct | Olivocerebellar tract | Fiber bundle |
| 253 | 8n | Vestibulocochlear nerve | Fiber bundle |
| 231 | stt | Spinal trigeminal tract_5th | Fiber bundle |
| 69 | fr | Fasciculus retroflexus | Fiber bundle |
| Cerebellum | |||
| 108 | I | Cerebellar lobule I | Lobe |
| 109 | II | Cerebellar lobule II | Lobe |
| 110 | III | Cerebellar lobule III | Lobe |
| 111 | IV | Cerebellar lobule IV | Lobe |
| 112 | V | Cerebellar lobule V | Lobe |
| 113 | VI | Cerebellar lobule VI | Lobe |
| 114 | VII | Cerebellar lobule VII | Lobe |
| 115 | VIII | Cerebellar lobule VIII | Lobe |
| 116 | IX | Cerebellar lobule IX | Lobe |
| 117 | X | Cerebellar lobule X | Lobe |
| 118 | Par_p | Paramedian lobule posterior part | Lobe |
| 119 | Par_a | Paramedian lobule anterior part | Lobe |
| 120 | Cr_II | Crus II of the ansiform lobule | Lobe |
| 121 | Cr_I | Crus I of the ansiform lobule | Lobe |
| 125 | Fl | Flocculus | Lobe |
| 233 | PFl | Paraflocculus | Lobe |
| 222 | Sim_a | Anterior part of the simple lobule | Lobe |
| 223 | Sim_p | Posterior part of the simple lobule | Lobe |
| 61 | DN | Dentate nucleus | Deep cerebellar nuclei |
| 62 | AIN | Anterior interposed nucleus | Deep cerebellar nuclei |
| 63 | PIN | Posterior interposed nucleus | Deep cerebellar nuclei |
| 64 | FN | Fastigial nucleus | Deep cerebellar nuclei |
| Limbic region (Amygdala) | |||
| 237 | L | Lateral nucleus of amygdala | |
| 82 | Bmc | Basal nucleus of amygdala, magnocellular subdivision | |
| 83 | Bi | Basal nucleus of amygdala, intermediate subdivision | |
| 84 | Bpc | Basal nucleus of amygdala, parvicellular subdivision | |
| 85 | ABmc | Accessory basal nucleus of amygdala, magnocellular | |
| 86 | ABpc | Accessory basal nucleus of amygdala, parvicellular | |
| 238 | ABs | Accessory basal nucleus of amygdala, superficial division | |
| 311 | AAA | Anterior amygdaloid area | |
| 87 | COa | Anterior cortical nucleus | |
| 97 | COp | Posterior cortical nucleus | |
| 89 | NLOT | Nucleus of the lateral olfactory tract | |
| 508 | PACo/Pir | Periamygdaloid cortex o/piriform cortex | |
| 509 | PAC2 | Periamygdaloid cortex 2 | |
| 90 | PAC3 | Periamygdaloid cortex 3 | |
| 91 | PACs | Periamygdaloid cortex, sulcal portion | |
| 93 | ME | Medial nucleus of amygdala | |
| 95 | AHA | Amygdalohippocampal area | |
| 96 | PL_prime | Paralaminar nucleus in amygdala | |
| 239 | CEm | Central nucleus of amygdala, medial division | |
| 240 | CEl | Central nucleus of amygdala, lateral division | |
| 241 | CEc | Central nucleus of amygdala, capsular division | |
| Allocortical region (Hippocampal formation) and associated fiber bundle | |||
| 242 | FD | Fascia dentata (granule cell layer) | Dentate Gyrus subregions |
| 71 | CA1 | CA1 subfield of hippocampus | Cornu Ammonis (CA) |
| 72 | CA2 | CA2 subfield of hippocampus | Cornu Ammonis (CA) |
| 73 | CA3 | CA3 subfield of hippocampus | Cornu Ammonis (CA) |
| 74 | CA4 | CA4 subfield of hippocampus | Cornu Ammonis (CA) |
| 76 | preS | Presubiculum | Subicular region |
| 77 | Sub | Subiculum | Subicular region |
| 78 | proS | Prosubiculum | Subicular region |
| 79 | paraS | Parasubiculum | Subicular region |
| 137 | f | Fornix | Fiber bundle |
| Basal forebrain (Cholinergic cell groups) | |||
| 209 | Ch1 | Cholinergic cell group 1 | Basal forebrain |
| 202 | Ch2 | Cholinergic cell group 2 (nucleus of vertical limb of the diagonal band) | Basal forebrain |
| 203 | Ch3 | Cholinergic cell group 3 (nucleus of horizontal limb of the diagonal band) | Basal forebrain |
| 204 | Ch4_al | Cholinergic cell group 4, anterior lateral division (nucleus basalis of Meynert) | Basal forebrain |
| 205 | Ch4_am | Cholinergic cell group 4, anterior medial division (nucleus basalis of Meynert) | Basal forebrain |
| 206 | Ch4_id | Cholinergic cell group 4, intermedio-dorsal division (nucleus basalis of Meynert) | Basal forebrain |
| 207 | Ch4_iv | Cholinergic cell group 4, intermedio-ventral division (nucleus basalis of Meynert) | Basal forebrain |
| 208 | Ch4_p | Cholinergic cell group 4, posterior division | Basal forebrain |
| Bed nucleus of stria terminalis | |||
| 196 | BSTM | Medial bed nucleus of stria terminalis | Bed nucleus of stria terminalis |
| 197 | BSTLcn | Lateral bed nucleus of stria terminalis, central subdivision | Bed nucleus of stria terminalis |
| 198 | BSTP | Posterior bed nucleus of stria terminalis | Bed nucleus of stria terminalis |
| 200 | BSTLc | Lateral bed nucleus of stria terminalis, capsular subdivision | Bed nucleus of stria terminalis |
| 201 | BSTLj | Lateral bed nucleus of stria terminalis, juxtacapsular subdivision | Bed nucleus of stria terminalis |
| Subcortical Atlas of Marmoset (SAM) V1.0 - SUMMARY | |||
| Total number of subcortical areas segmented: 251 | |||
| Segmented gray matter structures: 211 | |||
| Segmented white matter fiber bundles: 40 | |||
Note: The 210 subcortical gray matter structures also include non-subcortical regions such as the hippocampal formation and the cerebellum.