diff --git a/spimquant/config/snakebids.yml b/spimquant/config/snakebids.yml index ac66a7c..b5f952d 100644 --- a/spimquant/config/snakebids.yml +++ b/spimquant/config/snakebids.yml @@ -266,6 +266,15 @@ templates: roi198: dseg: 'tpl-ABAv3/tpl-ABAv3_seg-roi198_dseg.nii.gz' tsv: 'tpl-ABAv3/tpl-ABAv3_seg-roi198_dseg.tsv' + coarse: + dseg: 'tpl-ABAv3/tpl-ABAv3_seg-coarse_dseg.nii.gz' + tsv: 'tpl-ABAv3/tpl-ABAv3_seg-coarse_dseg.tsv' + mid: + dseg: 'tpl-ABAv3/tpl-ABAv3_seg-mid_dseg.nii.gz' + tsv: 'tpl-ABAv3/tpl-ABAv3_seg-mid_dseg.tsv' + fine: + dseg: 'tpl-ABAv3/tpl-ABAv3_seg-fine_dseg.nii.gz' + tsv: 'tpl-ABAv3/tpl-ABAv3_seg-fine_dseg.tsv' MouseIn: # MP2RAGE inv1 chosen since its most similar to the MT GRE I had on hand.. better to create a # new template later.. diff --git a/spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-coarse_dseg.nii.gz b/spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-coarse_dseg.nii.gz new file mode 100644 index 0000000..1205e81 Binary files /dev/null and b/spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-coarse_dseg.nii.gz differ diff --git a/spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-coarse_dseg.tsv b/spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-coarse_dseg.tsv new file mode 100644 index 0000000..96033c2 --- /dev/null +++ b/spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-coarse_dseg.tsv @@ -0,0 +1,25 @@ +index name abbreviation +1 L_Isocortex L_Isocortex +2 R_Isocortex R_Isocortex +3 L_Olfactory areas L_OLF +4 R_Olfactory areas R_OLF +5 L_Hippocampal formation L_HPF +6 R_Hippocampal formation R_HPF +7 L_Cortical subplate L_CTXsp +8 R_Cortical subplate R_CTXsp +9 L_Striatum L_STR +10 R_Striatum R_STR +11 L_Pallidum L_PAL +12 R_Pallidum R_PAL +13 L_Thalamus L_TH +14 R_Thalamus R_TH +15 L_Hypothalamus L_HY +16 R_Hypothalamus R_HY +17 L_Midbrain L_MB +18 R_Midbrain R_MB +19 L_Pons L_P +20 R_Pons R_P +21 L_Medulla L_MY +22 R_Medulla R_MY +23 L_Cerebellum L_CB +24 R_Cerebellum R_CB diff --git a/spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-fine_dseg.nii.gz b/spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-fine_dseg.nii.gz new file mode 100644 index 0000000..1579507 Binary files /dev/null and b/spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-fine_dseg.nii.gz differ diff --git a/spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-fine_dseg.tsv b/spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-fine_dseg.tsv new file mode 100644 index 0000000..cd7c613 --- /dev/null +++ b/spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-fine_dseg.tsv @@ -0,0 +1,633 @@ +index name abbreviation +1 "L_Frontal pole cerebral cortex" L_FRP +2 "R_Frontal pole cerebral cortex" R_FRP +3 L_Primary motor area L_MOp +4 R_Primary motor area R_MOp +5 L_Secondary motor area L_MOs +6 R_Secondary motor area R_MOs +7 "L_Primary somatosensory area nose" L_SSp-n +8 "R_Primary somatosensory area nose" R_SSp-n +9 "L_Primary somatosensory area barrel field" L_SSp-bfd +10 "R_Primary somatosensory area barrel field" R_SSp-bfd +11 "L_Primary somatosensory area lower limb" L_SSp-ll +12 "R_Primary somatosensory area lower limb" R_SSp-ll +13 "L_Primary somatosensory area mouth" L_SSp-m +14 "R_Primary somatosensory area mouth" R_SSp-m +15 "L_Primary somatosensory area upper limb" L_SSp-ul +16 "R_Primary somatosensory area upper limb" R_SSp-ul +17 "L_Primary somatosensory area trunk" L_SSp-tr +18 "R_Primary somatosensory area trunk" R_SSp-tr +19 "L_Primary somatosensory area unassigned" L_SSp-un +20 "R_Primary somatosensory area unassigned" R_SSp-un +21 L_Supplemental somatosensory area L_SSs +22 R_Supplemental somatosensory area R_SSs +23 L_Gustatory areas L_GU +24 R_Gustatory areas R_GU +25 L_Visceral area L_VISC +26 R_Visceral area R_VISC +27 L_Dorsal auditory area L_AUDd +28 R_Dorsal auditory area R_AUDd +29 L_Primary auditory area L_AUDp +30 R_Primary auditory area R_AUDp +31 L_Posterior auditory area L_AUDpo +32 R_Posterior auditory area R_AUDpo +33 L_Ventral auditory area L_AUDv +34 R_Ventral auditory area R_AUDv +35 L_Anterolateral visual area L_VISal +36 R_Anterolateral visual area R_VISal +37 L_Anteromedial visual area L_VISam +38 R_Anteromedial visual area R_VISam +39 L_Lateral visual area L_VISl +40 R_Lateral visual area R_VISl +41 L_Primary visual area L_VISp +42 R_Primary visual area R_VISp +43 L_Posterolateral visual area L_VISpl +44 R_Posterolateral visual area R_VISpl +45 L_posteromedial visual area L_VISpm +46 R_posteromedial visual area R_VISpm +47 L_Laterointermediate area L_VISli +48 R_Laterointermediate area R_VISli +49 L_Postrhinal area L_VISpor +50 R_Postrhinal area R_VISpor +51 "L_Anterior cingulate area dorsal part" L_ACAd +52 "R_Anterior cingulate area dorsal part" R_ACAd +53 "L_Anterior cingulate area ventral part" L_ACAv +54 "R_Anterior cingulate area ventral part" R_ACAv +55 L_Prelimbic area L_PL +56 R_Prelimbic area R_PL +57 L_Infralimbic area L_ILA +58 R_Infralimbic area R_ILA +59 "L_Orbital area lateral part" L_ORBl +60 "R_Orbital area lateral part" R_ORBl +61 "L_Orbital area medial part" L_ORBm +62 "R_Orbital area medial part" R_ORBm +63 "L_Orbital area ventrolateral part" L_ORBvl +64 "R_Orbital area ventrolateral part" R_ORBvl +65 "L_Agranular insular area dorsal part" L_AId +66 "R_Agranular insular area dorsal part" R_AId +67 "L_Agranular insular area posterior part" L_AIp +68 "R_Agranular insular area posterior part" R_AIp +69 "L_Agranular insular area ventral part" L_AIv +70 "R_Agranular insular area ventral part" R_AIv +71 "L_Retrosplenial area lateral agranular part" L_RSPagl +72 "R_Retrosplenial area lateral agranular part" R_RSPagl +73 "L_Retrosplenial area dorsal part" L_RSPd +74 "R_Retrosplenial area dorsal part" R_RSPd +75 "L_Retrosplenial area ventral part" L_RSPv +76 "R_Retrosplenial area ventral part" R_RSPv +77 L_Anterior area L_VISa +78 R_Anterior area R_VISa +79 L_Rostrolateral visual area L_VISrl +80 R_Rostrolateral visual area R_VISrl +81 L_Temporal association areas L_TEa +82 R_Temporal association areas R_TEa +83 L_Perirhinal area L_PERI +84 R_Perirhinal area R_PERI +85 L_Ectorhinal area L_ECT +86 R_Ectorhinal area R_ECT +87 L_Main olfactory bulb L_MOB +88 R_Main olfactory bulb R_MOB +89 L_Accessory olfactory bulb L_AOB +90 R_Accessory olfactory bulb R_AOB +91 L_Anterior olfactory nucleus L_AON +92 R_Anterior olfactory nucleus R_AON +93 L_Taenia tecta L_TT +94 R_Taenia tecta R_TT +95 L_Dorsal peduncular area L_DP +96 R_Dorsal peduncular area R_DP +97 L_Piriform area L_PIR +98 R_Piriform area R_PIR +99 L_Nucleus of the lateral olfactory tract L_NLOT +100 R_Nucleus of the lateral olfactory tract R_NLOT +101 "L_Cortical amygdalar area anterior part" L_COAa +102 "R_Cortical amygdalar area anterior part" R_COAa +103 "L_Cortical amygdalar area posterior part" L_COAp +104 "R_Cortical amygdalar area posterior part" R_COAp +105 L_Piriform-amygdalar area L_PAA +106 R_Piriform-amygdalar area R_PAA +107 L_Postpiriform transition area L_TR +108 R_Postpiriform transition area R_TR +109 L_Field CA1 L_CA1 +110 R_Field CA1 R_CA1 +111 L_Field CA2 L_CA2 +112 R_Field CA2 R_CA2 +113 L_Field CA3 L_CA3 +114 R_Field CA3 R_CA3 +115 L_Dentate gyrus L_DG +116 R_Dentate gyrus R_DG +117 L_Fasciola cinerea L_FC +118 R_Fasciola cinerea R_FC +119 L_Induseum griseum L_IG +120 R_Induseum griseum R_IG +121 "L_Entorhinal area lateral part" L_ENTl +122 "R_Entorhinal area lateral part" R_ENTl +123 "L_Entorhinal area medial part dorsal zone" L_ENTm +124 "R_Entorhinal area medial part dorsal zone" R_ENTm +125 L_Parasubiculum L_PAR +126 R_Parasubiculum R_PAR +127 L_Postsubiculum L_POST +128 R_Postsubiculum R_POST +129 L_Presubiculum L_PRE +130 R_Presubiculum R_PRE +131 L_Subiculum L_SUB +132 R_Subiculum R_SUB +133 L_Prosubiculum L_ProS +134 R_Prosubiculum R_ProS +135 L_Hippocampo-amygdalar transition area L_HATA +136 R_Hippocampo-amygdalar transition area R_HATA +137 L_Area prostriata L_APr +138 R_Area prostriata R_APr +139 L_Claustrum L_CLA +140 R_Claustrum R_CLA +141 "L_Endopiriform nucleus dorsal part" L_EPd +142 "R_Endopiriform nucleus dorsal part" R_EPd +143 "L_Endopiriform nucleus ventral part" L_EPv +144 "R_Endopiriform nucleus ventral part" R_EPv +145 L_Lateral amygdalar nucleus L_LA +146 R_Lateral amygdalar nucleus R_LA +147 L_Basolateral amygdalar nucleus L_BLA +148 R_Basolateral amygdalar nucleus R_BLA +149 L_Basomedial amygdalar nucleus L_BMA +150 R_Basomedial amygdalar nucleus R_BMA +151 L_Posterior amygdalar nucleus L_PA +152 R_Posterior amygdalar nucleus R_PA +153 L_Caudoputamen L_CP +154 R_Caudoputamen R_CP +155 L_Nucleus accumbens L_ACB +156 R_Nucleus accumbens R_ACB +157 L_Fundus of striatum L_FS +158 R_Fundus of striatum R_FS +159 L_Olfactory tubercle L_OT +160 R_Olfactory tubercle R_OT +161 "L_Lateral septal nucleus caudal (caudodorsal) part" L_LSc +162 "R_Lateral septal nucleus caudal (caudodorsal) part" R_LSc +163 "L_Lateral septal nucleus rostral (rostroventral) part" L_LSr +164 "R_Lateral septal nucleus rostral (rostroventral) part" R_LSr +165 "L_Lateral septal nucleus ventral part" L_LSv +166 "R_Lateral septal nucleus ventral part" R_LSv +167 L_Septofimbrial nucleus L_SF +168 R_Septofimbrial nucleus R_SF +169 L_Septohippocampal nucleus L_SH +170 R_Septohippocampal nucleus R_SH +171 L_Anterior amygdalar area L_AAA +172 R_Anterior amygdalar area R_AAA +173 L_Bed nucleus of the accessory olfactory tract L_BA +174 R_Bed nucleus of the accessory olfactory tract R_BA +175 L_Central amygdalar nucleus L_CEA +176 R_Central amygdalar nucleus R_CEA +177 L_Intercalated amygdalar nucleus L_IA +178 R_Intercalated amygdalar nucleus R_IA +179 L_Medial amygdalar nucleus L_MEA +180 R_Medial amygdalar nucleus R_MEA +181 "L_Globus pallidus external segment" L_GPe +182 "R_Globus pallidus external segment" R_GPe +183 "L_Globus pallidus internal segment" L_GPi +184 "R_Globus pallidus internal segment" R_GPi +185 L_Substantia innominata L_SI +186 R_Substantia innominata R_SI +187 L_Magnocellular nucleus L_MA +188 R_Magnocellular nucleus R_MA +189 L_Medial septal nucleus L_MS +190 R_Medial septal nucleus R_MS +191 L_Diagonal band nucleus L_NDB +192 R_Diagonal band nucleus R_NDB +193 L_Triangular nucleus of septum L_TRS +194 R_Triangular nucleus of septum R_TRS +195 L_Bed nuclei of the stria terminalis L_BST +196 R_Bed nuclei of the stria terminalis R_BST +197 L_Bed nucleus of the anterior commissure L_BAC +198 R_Bed nucleus of the anterior commissure R_BAC +199 L_Ventral anterior-lateral complex of the thalamus L_VAL +200 R_Ventral anterior-lateral complex of the thalamus R_VAL +201 L_Ventral medial nucleus of the thalamus L_VM +202 R_Ventral medial nucleus of the thalamus R_VM +203 L_Ventral posterolateral nucleus of the thalamus L_VPL +204 R_Ventral posterolateral nucleus of the thalamus R_VPL +205 "L_Ventral posterolateral nucleus of the thalamus parvicellular part" L_VPLpc +206 "R_Ventral posterolateral nucleus of the thalamus parvicellular part" R_VPLpc +207 L_Ventral posteromedial nucleus of the thalamus L_VPM +208 R_Ventral posteromedial nucleus of the thalamus R_VPM +209 "L_Ventral posteromedial nucleus of the thalamus parvicellular part" L_VPMpc +210 "R_Ventral posteromedial nucleus of the thalamus parvicellular part" R_VPMpc +211 L_Posterior triangular thalamic nucleus L_PoT +212 R_Posterior triangular thalamic nucleus R_PoT +213 "L_Subparafascicular nucleus magnocellular part" L_SPFm +214 "R_Subparafascicular nucleus magnocellular part" R_SPFm +215 "L_Subparafascicular nucleus parvicellular part" L_SPFp +216 "R_Subparafascicular nucleus parvicellular part" R_SPFp +217 L_Subparafascicular area L_SPA +218 R_Subparafascicular area R_SPA +219 L_Peripeduncular nucleus L_PP +220 R_Peripeduncular nucleus R_PP +221 L_Medial geniculate complex L_MG +222 R_Medial geniculate complex R_MG +223 L_Dorsal part of the lateral geniculate complex L_LGd +224 R_Dorsal part of the lateral geniculate complex R_LGd +225 L_Lateral posterior nucleus of the thalamus L_LP +226 R_Lateral posterior nucleus of the thalamus R_LP +227 L_Posterior complex of the thalamus L_PO +228 R_Posterior complex of the thalamus R_PO +229 L_Posterior limiting nucleus of the thalamus L_POL +230 R_Posterior limiting nucleus of the thalamus R_POL +231 L_Suprageniculate nucleus L_SGN +232 R_Suprageniculate nucleus R_SGN +233 L_Anteroventral nucleus of thalamus L_AV +234 R_Anteroventral nucleus of thalamus R_AV +235 L_Anteromedial nucleus L_AM +236 R_Anteromedial nucleus R_AM +237 L_Anterodorsal nucleus L_AD +238 R_Anterodorsal nucleus R_AD +239 L_Interanteromedial nucleus of the thalamus L_IAM +240 R_Interanteromedial nucleus of the thalamus R_IAM +241 L_Interanterodorsal nucleus of the thalamus L_IAD +242 R_Interanterodorsal nucleus of the thalamus R_IAD +243 L_Lateral dorsal nucleus of thalamus L_LD +244 R_Lateral dorsal nucleus of thalamus R_LD +245 L_Intermediodorsal nucleus of the thalamus L_IMD +246 R_Intermediodorsal nucleus of the thalamus R_IMD +247 L_Mediodorsal nucleus of thalamus L_MD +248 R_Mediodorsal nucleus of thalamus R_MD +249 L_Submedial nucleus of the thalamus L_SMT +250 R_Submedial nucleus of the thalamus R_SMT +251 L_Perireunensis nucleus L_PR +252 R_Perireunensis nucleus R_PR +253 L_Paraventricular nucleus of the thalamus L_PVT +254 R_Paraventricular nucleus of the thalamus R_PVT +255 L_Parataenial nucleus L_PT +256 R_Parataenial nucleus R_PT +257 L_Nucleus of reuniens L_RE +258 R_Nucleus of reuniens R_RE +259 L_Xiphoid thalamic nucleus L_Xi +260 R_Xiphoid thalamic nucleus R_Xi +261 L_Rhomboid nucleus L_RH +262 R_Rhomboid nucleus R_RH +263 L_Central medial nucleus of the thalamus L_CM +264 R_Central medial nucleus of the thalamus R_CM +265 L_Paracentral nucleus L_PCN +266 R_Paracentral nucleus R_PCN +267 L_Central lateral nucleus of the thalamus L_CL +268 R_Central lateral nucleus of the thalamus R_CL +269 L_Parafascicular nucleus L_PF +270 R_Parafascicular nucleus R_PF +271 L_Posterior intralaminar thalamic nucleus L_PIL +272 R_Posterior intralaminar thalamic nucleus R_PIL +273 L_Reticular nucleus of the thalamus L_RT +274 R_Reticular nucleus of the thalamus R_RT +275 L_Intergeniculate leaflet of the lateral geniculate complex L_IGL +276 R_Intergeniculate leaflet of the lateral geniculate complex R_IGL +277 L_Intermediate geniculate nucleus L_IntG +278 R_Intermediate geniculate nucleus R_IntG +279 L_Ventral part of the lateral geniculate complex L_LGv +280 R_Ventral part of the lateral geniculate complex R_LGv +281 L_Subgeniculate nucleus L_SubG +282 R_Subgeniculate nucleus R_SubG +283 L_Medial habenula L_MH +284 R_Medial habenula R_MH +285 L_Lateral habenula L_LH +286 R_Lateral habenula R_LH +287 L_Supraoptic nucleus L_SO +288 R_Supraoptic nucleus R_SO +289 L_Accessory supraoptic group L_ASO +290 R_Accessory supraoptic group R_ASO +291 L_Paraventricular hypothalamic nucleus L_PVH +292 R_Paraventricular hypothalamic nucleus R_PVH +293 "L_Periventricular hypothalamic nucleus anterior part" L_PVa +294 "R_Periventricular hypothalamic nucleus anterior part" R_PVa +295 "L_Periventricular hypothalamic nucleus intermediate part" L_PVi +296 "R_Periventricular hypothalamic nucleus intermediate part" R_PVi +297 L_Arcuate hypothalamic nucleus L_ARH +298 R_Arcuate hypothalamic nucleus R_ARH +299 L_Anterodorsal preoptic nucleus L_ADP +300 R_Anterodorsal preoptic nucleus R_ADP +301 L_Anteroventral preoptic nucleus L_AVP +302 R_Anteroventral preoptic nucleus R_AVP +303 L_Anteroventral periventricular nucleus L_AVPV +304 R_Anteroventral periventricular nucleus R_AVPV +305 L_Dorsomedial nucleus of the hypothalamus L_DMH +306 R_Dorsomedial nucleus of the hypothalamus R_DMH +307 L_Median preoptic nucleus L_MEPO +308 R_Median preoptic nucleus R_MEPO +309 L_Medial preoptic area L_MPO +310 R_Medial preoptic area R_MPO +311 L_Vascular organ of the lamina terminalis L_OV +312 R_Vascular organ of the lamina terminalis R_OV +313 L_Posterodorsal preoptic nucleus L_PD +314 R_Posterodorsal preoptic nucleus R_PD +315 L_Parastrial nucleus L_PS +316 R_Parastrial nucleus R_PS +317 "L_Periventricular hypothalamic nucleus posterior part" L_PVp +318 "R_Periventricular hypothalamic nucleus posterior part" R_PVp +319 "L_Periventricular hypothalamic nucleus preoptic part" L_PVpo +320 "R_Periventricular hypothalamic nucleus preoptic part" R_PVpo +321 L_Subparaventricular zone L_SBPV +322 R_Subparaventricular zone R_SBPV +323 L_Suprachiasmatic nucleus L_SCH +324 R_Suprachiasmatic nucleus R_SCH +325 L_Subfornical organ L_SFO +326 R_Subfornical organ R_SFO +327 L_Ventromedial preoptic nucleus L_VMPO +328 R_Ventromedial preoptic nucleus R_VMPO +329 L_Ventrolateral preoptic nucleus L_VLPO +330 R_Ventrolateral preoptic nucleus R_VLPO +331 L_Anterior hypothalamic nucleus L_AHN +332 R_Anterior hypothalamic nucleus R_AHN +333 L_Lateral mammillary nucleus L_LM +334 R_Lateral mammillary nucleus R_LM +335 L_Medial mammillary nucleus L_MM +336 R_Medial mammillary nucleus R_MM +337 L_Supramammillary nucleus L_SUM +338 R_Supramammillary nucleus R_SUM +339 "L_Tuberomammillary nucleus dorsal part" L_TMd +340 "R_Tuberomammillary nucleus dorsal part" R_TMd +341 "L_Tuberomammillary nucleus ventral part" L_TMv +342 "R_Tuberomammillary nucleus ventral part" R_TMv +343 L_Medial preoptic nucleus L_MPN +344 R_Medial preoptic nucleus R_MPN +345 L_Dorsal premammillary nucleus L_PMd +346 R_Dorsal premammillary nucleus R_PMd +347 L_Ventral premammillary nucleus L_PMv +348 R_Ventral premammillary nucleus R_PMv +349 "L_Paraventricular hypothalamic nucleus descending division" L_PVHd +350 "R_Paraventricular hypothalamic nucleus descending division" R_PVHd +351 L_Ventromedial hypothalamic nucleus L_VMH +352 R_Ventromedial hypothalamic nucleus R_VMH +353 L_Posterior hypothalamic nucleus L_PH +354 R_Posterior hypothalamic nucleus R_PH +355 L_Lateral hypothalamic area L_LHA +356 R_Lateral hypothalamic area R_LHA +357 L_Lateral preoptic area L_LPO +358 R_Lateral preoptic area R_LPO +359 L_Preparasubthalamic nucleus L_PST +360 R_Preparasubthalamic nucleus R_PST +361 L_Parasubthalamic nucleus L_PSTN +362 R_Parasubthalamic nucleus R_PSTN +363 L_Perifornical nucleus L_PeF +364 R_Perifornical nucleus R_PeF +365 L_Retrochiasmatic area L_RCH +366 R_Retrochiasmatic area R_RCH +367 L_Subthalamic nucleus L_STN +368 R_Subthalamic nucleus R_STN +369 L_Tuberal nucleus L_TU +370 R_Tuberal nucleus R_TU +371 L_Zona incerta L_ZI +372 R_Zona incerta R_ZI +373 L_Median eminence L_ME +374 R_Median eminence R_ME +375 "L_Superior colliculus sensory related" L_SCs +376 "R_Superior colliculus sensory related" R_SCs +377 L_Inferior colliculus L_IC +378 R_Inferior colliculus R_IC +379 L_Nucleus of the brachium of the inferior colliculus L_NB +380 R_Nucleus of the brachium of the inferior colliculus R_NB +381 L_Nucleus sagulum L_SAG +382 R_Nucleus sagulum R_SAG +383 L_Parabigeminal nucleus L_PBG +384 R_Parabigeminal nucleus R_PBG +385 L_Midbrain trigeminal nucleus L_MEV +386 R_Midbrain trigeminal nucleus R_MEV +387 L_Subcommissural organ L_SCO +388 R_Subcommissural organ R_SCO +389 "L_Substantia nigra reticular part" L_SNr +390 "R_Substantia nigra reticular part" R_SNr +391 L_Ventral tegmental area L_VTA +392 R_Ventral tegmental area R_VTA +393 L_Paranigral nucleus L_PN +394 R_Paranigral nucleus R_PN +395 "L_Midbrain reticular nucleus retrorubral area" L_RR +396 "R_Midbrain reticular nucleus retrorubral area" R_RR +397 L_Midbrain reticular nucleus L_MRN +398 R_Midbrain reticular nucleus R_MRN +399 "L_Superior colliculus motor related" L_SCm +400 "R_Superior colliculus motor related" R_SCm +401 L_Periaqueductal gray L_PAG +402 R_Periaqueductal gray R_PAG +403 L_Anterior pretectal nucleus L_APN +404 R_Anterior pretectal nucleus R_APN +405 L_Medial pretectal area L_MPT +406 R_Medial pretectal area R_MPT +407 L_Nucleus of the optic tract L_NOT +408 R_Nucleus of the optic tract R_NOT +409 L_Nucleus of the posterior commissure L_NPC +410 R_Nucleus of the posterior commissure R_NPC +411 L_Olivary pretectal nucleus L_OP +412 R_Olivary pretectal nucleus R_OP +413 L_Posterior pretectal nucleus L_PPT +414 R_Posterior pretectal nucleus R_PPT +415 L_Cuneiform nucleus L_CUN +416 R_Cuneiform nucleus R_CUN +417 L_Red nucleus L_RN +418 R_Red nucleus R_RN +419 L_Oculomotor nucleus L_III +420 R_Oculomotor nucleus R_III +421 L_Medial accesory oculomotor nucleus L_MA3 +422 R_Medial accesory oculomotor nucleus R_MA3 +423 L_Edinger-Westphal nucleus L_EW +424 R_Edinger-Westphal nucleus R_EW +425 L_Trochlear nucleus L_IV +426 R_Trochlear nucleus R_IV +427 L_Paratrochlear nucleus L_Pa4 +428 R_Paratrochlear nucleus R_Pa4 +429 L_Ventral tegmental nucleus L_VTN +430 R_Ventral tegmental nucleus R_VTN +431 L_Anterior tegmental nucleus L_AT +432 R_Anterior tegmental nucleus R_AT +433 L_Lateral terminal nucleus of the accessory optic tract L_LT +434 R_Lateral terminal nucleus of the accessory optic tract R_LT +435 L_Dorsal terminal nucleus of the accessory optic tract L_DT +436 R_Dorsal terminal nucleus of the accessory optic tract R_DT +437 L_Medial terminal nucleus of the accessory optic tract L_MT +438 R_Medial terminal nucleus of the accessory optic tract R_MT +439 "L_Substantia nigra compact part" L_SNc +440 "R_Substantia nigra compact part" R_SNc +441 L_Pedunculopontine nucleus L_PPN +442 R_Pedunculopontine nucleus R_PPN +443 L_Interfascicular nucleus raphe L_IF +444 R_Interfascicular nucleus raphe R_IF +445 L_Interpeduncular nucleus L_IPN +446 R_Interpeduncular nucleus R_IPN +447 L_Rostral linear nucleus raphe L_RL +448 R_Rostral linear nucleus raphe R_RL +449 L_Central linear nucleus raphe L_CLI +450 R_Central linear nucleus raphe R_CLI +451 L_Dorsal nucleus raphe L_DR +452 R_Dorsal nucleus raphe R_DR +453 L_Nucleus of the lateral lemniscus L_NLL +454 R_Nucleus of the lateral lemniscus R_NLL +455 L_Principal sensory nucleus of the trigeminal L_PSV +456 R_Principal sensory nucleus of the trigeminal R_PSV +457 L_Parabrachial nucleus L_PB +458 R_Parabrachial nucleus R_PB +459 L_Superior olivary complex L_SOC +460 R_Superior olivary complex R_SOC +461 L_Barrington's nucleus L_B +462 R_Barrington's nucleus R_B +463 L_Dorsal tegmental nucleus L_DTN +464 R_Dorsal tegmental nucleus R_DTN +465 L_Posterodorsal tegmental nucleus L_PDTg +466 R_Posterodorsal tegmental nucleus R_PDTg +467 L_Pontine central gray L_PCG +468 R_Pontine central gray R_PCG +469 L_Pontine gray L_PG +470 R_Pontine gray R_PG +471 "L_Pontine reticular nucleus caudal part" L_PRNc +472 "R_Pontine reticular nucleus caudal part" R_PRNc +473 L_Supragenual nucleus L_SG +474 R_Supragenual nucleus R_SG +475 L_Supratrigeminal nucleus L_SUT +476 R_Supratrigeminal nucleus R_SUT +477 L_Tegmental reticular nucleus L_TRN +478 R_Tegmental reticular nucleus R_TRN +479 L_Motor nucleus of trigeminal L_V +480 R_Motor nucleus of trigeminal R_V +481 L_Peritrigeminal zone L_P5 +482 R_Peritrigeminal zone R_P5 +483 L_Accessory trigeminal nucleus L_Acs5 +484 R_Accessory trigeminal nucleus R_Acs5 +485 L_Parvicellular motor 5 nucleus L_PC5 +486 R_Parvicellular motor 5 nucleus R_PC5 +487 L_Intertrigeminal nucleus L_I5 +488 R_Intertrigeminal nucleus R_I5 +489 L_Superior central nucleus raphe L_CS +490 R_Superior central nucleus raphe R_CS +491 L_Locus ceruleus L_LC +492 R_Locus ceruleus R_LC +493 L_Laterodorsal tegmental nucleus L_LDT +494 R_Laterodorsal tegmental nucleus R_LDT +495 L_Nucleus incertus L_NI +496 R_Nucleus incertus R_NI +497 L_Pontine reticular nucleus L_PRNr +498 R_Pontine reticular nucleus R_PRNr +499 L_Nucleus raphe pontis L_RPO +500 R_Nucleus raphe pontis R_RPO +501 L_Subceruleus nucleus L_SLC +502 R_Subceruleus nucleus R_SLC +503 L_Sublaterodorsal nucleus L_SLD +504 R_Sublaterodorsal nucleus R_SLD +505 L_Area postrema L_AP +506 R_Area postrema R_AP +507 L_Dorsal cochlear nucleus L_DCO +508 R_Dorsal cochlear nucleus R_DCO +509 L_Ventral cochlear nucleus L_VCO +510 R_Ventral cochlear nucleus R_VCO +511 L_Cuneate nucleus L_CU +512 R_Cuneate nucleus R_CU +513 L_Gracile nucleus L_GR +514 R_Gracile nucleus R_GR +515 L_External cuneate nucleus L_ECU +516 R_External cuneate nucleus R_ECU +517 L_Nucleus of the trapezoid body L_NTB +518 R_Nucleus of the trapezoid body R_NTB +519 L_Nucleus of the solitary tract L_NTS +520 R_Nucleus of the solitary tract R_NTS +521 "L_Spinal nucleus of the trigeminal caudal part" L_SPVC +522 "R_Spinal nucleus of the trigeminal caudal part" R_SPVC +523 "L_Spinal nucleus of the trigeminal interpolar part" L_SPVI +524 "R_Spinal nucleus of the trigeminal interpolar part" R_SPVI +525 "L_Spinal nucleus of the trigeminal oral part" L_SPVO +526 "R_Spinal nucleus of the trigeminal oral part" R_SPVO +527 L_Paratrigeminal nucleus L_Pa5 +528 R_Paratrigeminal nucleus R_Pa5 +529 L_Abducens nucleus L_VI +530 R_Abducens nucleus R_VI +531 L_Facial motor nucleus L_VII +532 R_Facial motor nucleus R_VII +533 L_Accessory facial motor nucleus L_ACVII +534 R_Accessory facial motor nucleus R_ACVII +535 L_Nucleus ambiguus L_AMB +536 R_Nucleus ambiguus R_AMB +537 L_Dorsal motor nucleus of the vagus nerve L_DMX +538 R_Dorsal motor nucleus of the vagus nerve R_DMX +539 L_Gigantocellular reticular nucleus L_GRN +540 R_Gigantocellular reticular nucleus R_GRN +541 L_Infracerebellar nucleus L_ICB +542 R_Infracerebellar nucleus R_ICB +543 L_Inferior olivary complex L_IO +544 R_Inferior olivary complex R_IO +545 L_Intermediate reticular nucleus L_IRN +546 R_Intermediate reticular nucleus R_IRN +547 L_Inferior salivatory nucleus L_ISN +548 R_Inferior salivatory nucleus R_ISN +549 L_Linear nucleus of the medulla L_LIN +550 R_Linear nucleus of the medulla R_LIN +551 L_Lateral reticular nucleus L_LRN +552 R_Lateral reticular nucleus R_LRN +553 L_Magnocellular reticular nucleus L_MARN +554 R_Magnocellular reticular nucleus R_MARN +555 L_Medullary reticular nucleus L_MDRN +556 R_Medullary reticular nucleus R_MDRN +557 "L_Medullary reticular nucleus dorsal part" L_MDRNd +558 "R_Medullary reticular nucleus dorsal part" R_MDRNd +559 "L_Medullary reticular nucleus ventral part" L_MDRNv +560 "R_Medullary reticular nucleus ventral part" R_MDRNv +561 L_Parvicellular reticular nucleus L_PARN +562 R_Parvicellular reticular nucleus R_PARN +563 L_Parasolitary nucleus L_PAS +564 R_Parasolitary nucleus R_PAS +565 "L_Paragigantocellular reticular nucleus dorsal part" L_PGRNd +566 "R_Paragigantocellular reticular nucleus dorsal part" R_PGRNd +567 "L_Paragigantocellular reticular nucleus lateral part" L_PGRNl +568 "R_Paragigantocellular reticular nucleus lateral part" R_PGRNl +569 L_Nucleus of Roller L_NR +570 R_Nucleus of Roller R_NR +571 L_Nucleus prepositus L_PRP +572 R_Nucleus prepositus R_PRP +573 L_Parapyramidal nucleus L_PPY +574 R_Parapyramidal nucleus R_PPY +575 L_Lateral vestibular nucleus L_LAV +576 R_Lateral vestibular nucleus R_LAV +577 L_Medial vestibular nucleus L_MV +578 R_Medial vestibular nucleus R_MV +579 L_Spinal vestibular nucleus L_SPIV +580 R_Spinal vestibular nucleus R_SPIV +581 L_Superior vestibular nucleus L_SUV +582 R_Superior vestibular nucleus R_SUV +583 L_Nucleus x L_x +584 R_Nucleus x R_x +585 L_Hypoglossal nucleus L_XII +586 R_Hypoglossal nucleus R_XII +587 L_Nucleus y L_y +588 R_Nucleus y R_y +589 L_Nucleus raphe magnus L_RM +590 R_Nucleus raphe magnus R_RM +591 L_Nucleus raphe pallidus L_RPA +592 R_Nucleus raphe pallidus R_RPA +593 L_Nucleus raphe obscurus L_RO +594 R_Nucleus raphe obscurus R_RO +595 L_Lingula (I) L_LING +596 R_Lingula (I) R_LING +597 L_Central lobule L_CENT +598 R_Central lobule R_CENT +599 L_Culmen L_CUL +600 R_Culmen R_CUL +601 L_Declive (VI) L_DEC +602 R_Declive (VI) R_DEC +603 L_Folium-tuber vermis (VII) L_FOTU +604 R_Folium-tuber vermis (VII) R_FOTU +605 L_Pyramus (VIII) L_PYR +606 R_Pyramus (VIII) R_PYR +607 L_Uvula (IX) L_UVU +608 R_Uvula (IX) R_UVU +609 L_Nodulus (X) L_NOD +610 R_Nodulus (X) R_NOD +611 L_Simple lobule L_SIM +612 R_Simple lobule R_SIM +613 L_Ansiform lobule L_AN +614 R_Ansiform lobule R_AN +615 L_Paramedian lobule L_PRM +616 R_Paramedian lobule R_PRM +617 L_Copula pyramidis L_COPY +618 R_Copula pyramidis R_COPY +619 L_Paraflocculus L_PFL +620 R_Paraflocculus R_PFL +621 L_Flocculus L_FL +622 R_Flocculus R_FL +623 L_Fastigial nucleus L_FN +624 R_Fastigial nucleus R_FN +625 L_Interposed nucleus L_IP +626 R_Interposed nucleus R_IP +627 L_Dentate nucleus L_DN +628 R_Dentate nucleus R_DN +629 L_Vestibulocerebellar nucleus L_VeCB +630 R_Vestibulocerebellar nucleus R_VeCB +631 L_fiber tracts L_fiber tracts +632 R_fiber tracts R_fiber tracts diff --git a/spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-mid_dseg.nii.gz b/spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-mid_dseg.nii.gz new file mode 100644 index 0000000..eacfedc Binary files /dev/null and b/spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-mid_dseg.nii.gz differ diff --git a/spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-mid_dseg.tsv b/spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-mid_dseg.tsv new file mode 100644 index 0000000..77c6b1d --- /dev/null +++ b/spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-mid_dseg.tsv @@ -0,0 +1,103 @@ +index name abbreviation +1 "L_Frontal pole cerebral cortex" L_FRP +2 "R_Frontal pole cerebral cortex" R_FRP +3 L_Somatomotor areas L_MO +4 R_Somatomotor areas R_MO +5 L_Somatosensory areas L_SS +6 R_Somatosensory areas R_SS +7 L_Gustatory areas L_GU +8 R_Gustatory areas R_GU +9 L_Visceral area L_VISC +10 R_Visceral area R_VISC +11 L_Auditory areas L_AUD +12 R_Auditory areas R_AUD +13 L_Visual areas L_VIS +14 R_Visual areas R_VIS +15 L_Anterior cingulate area L_ACA +16 R_Anterior cingulate area R_ACA +17 L_Prelimbic area L_PL +18 R_Prelimbic area R_PL +19 L_Infralimbic area L_ILA +20 R_Infralimbic area R_ILA +21 L_Orbital area L_ORB +22 R_Orbital area R_ORB +23 L_Agranular insular area L_AI +24 R_Agranular insular area R_AI +25 L_Retrosplenial area L_RSP +26 R_Retrosplenial area R_RSP +27 L_Posterior parietal association areas L_PTLp +28 R_Posterior parietal association areas R_PTLp +29 L_Temporal association areas L_TEa +30 R_Temporal association areas R_TEa +31 L_Perirhinal area L_PERI +32 R_Perirhinal area R_PERI +33 L_Ectorhinal area L_ECT +34 R_Ectorhinal area R_ECT +35 L_Olfactory areas L_OLF +36 R_Olfactory areas R_OLF +37 L_Ammon's horn L_CA +38 R_Ammon's horn R_CA +39 L_Dentate gyrus L_DG +40 R_Dentate gyrus R_DG +41 L_Fasciola cinerea L_FC +42 R_Fasciola cinerea R_FC +43 L_Induseum griseum L_IG +44 R_Induseum griseum R_IG +45 L_Retrohippocampal region L_RHP +46 R_Retrohippocampal region R_RHP +47 L_Cortical subplate L_CTXsp +48 R_Cortical subplate R_CTXsp +49 L_Striatum dorsal region L_STRd +50 R_Striatum dorsal region R_STRd +51 L_Striatum ventral region L_STRv +52 R_Striatum ventral region R_STRv +53 L_Lateral septal complex L_LSX +54 R_Lateral septal complex R_LSX +55 L_Striatum-like amygdalar nuclei L_sAMY +56 R_Striatum-like amygdalar nuclei R_sAMY +57 "L_Pallidum dorsal region" L_PALd +58 "R_Pallidum dorsal region" R_PALd +59 "L_Pallidum ventral region" L_PALv +60 "R_Pallidum ventral region" R_PALv +61 "L_Pallidum medial region" L_PALm +62 "R_Pallidum medial region" R_PALm +63 "L_Pallidum caudal region" L_PALc +64 "R_Pallidum caudal region" R_PALc +65 "L_Thalamus sensory-motor cortex related" L_DORsm +66 "R_Thalamus sensory-motor cortex related" R_DORsm +67 "L_Thalamus polymodal association cortex related" L_DORpm +68 "R_Thalamus polymodal association cortex related" R_DORpm +69 L_Periventricular zone L_PVZ +70 R_Periventricular zone R_PVZ +71 L_Periventricular region L_PVR +72 R_Periventricular region R_PVR +73 L_Hypothalamic medial zone L_MEZ +74 R_Hypothalamic medial zone R_MEZ +75 L_Hypothalamic lateral zone L_LZ +76 R_Hypothalamic lateral zone R_LZ +77 L_Median eminence L_ME +78 R_Median eminence R_ME +79 "L_Midbrain sensory related" L_MBsen +80 "R_Midbrain sensory related" R_MBsen +81 "L_Midbrain motor related" L_MBmot +82 "R_Midbrain motor related" R_MBmot +83 "L_Midbrain behavioral state related" L_MBsta +84 "R_Midbrain behavioral state related" R_MBsta +85 "L_Pons sensory related" L_P-sen +86 "R_Pons sensory related" R_P-sen +87 "L_Pons motor related" L_P-mot +88 "R_Pons motor related" R_P-mot +89 "L_Pons behavioral state related" L_P-sat +90 "R_Pons behavioral state related" R_P-sat +91 "L_Medulla sensory related" L_MY-sen +92 "R_Medulla sensory related" R_MY-sen +93 "L_Medulla motor related" L_MY-mot +94 "R_Medulla motor related" R_MY-mot +95 "L_Medulla behavioral state related" L_MY-sat +96 "R_Medulla behavioral state related" R_MY-sat +97 L_Vermal regions L_VERM +98 R_Vermal regions R_VERM +99 L_Hemispheric regions L_HEM +100 R_Hemispheric regions R_HEM +101 L_Cerebellar nuclei L_CBN +102 R_Cerebellar nuclei R_CBN