updated input and output

input/C57BL6_mouse/ABA.license.txt

@@ -0,0 +1,25 @@
+The ABA here was nonlinearly warpped from CCFv3 to DSI Studio's C57BL/6 space.
+
+Please note that ABA's CCFv3 space has a substantial shape differences from most C57BL/6 mouses, and the anterior tip is missing.
+The modified ABA in this package corrected these two issues.
+
+
+Data source:
+
+https://scalablebrainatlas.incf.org/mouse/ABA_v3
+
+About ABA
+
+The Allen Reference Atlas is created by the Allen Institute for Brain Science. It is published on the web (3D Coronal version) and in print: H.W. Dong, The Allen Reference Atlas, (Book + CD-ROM): A Digital Color Brain Atlas of the C57BL/6J Male Mouse, Wiley, 2008.
+
+The digital version of the atlas has been symmetrized with respect to the midline, and has been through two stages of refinement since its initial conception. This is the third version of the atlas, known as Common Coordinate Framework version 3 (white paper), downloaded in 2017. The raw data file was converted to a Nifti file in RAS-orientation with voxel dimensions of 0.025 mm. The Allen Institute does not define an origin for its atlases, and therefore we took the freedom to set it as close as possible to the origin of the Waxholm mouse atlas. It is set to voxel [229,314,114] (where the first voxel has index 1 in each dimension).
+
+The original, manually annotated sections can be viewed using the "AllenAtlas" plugin.
+
+The volumetric atlas also features in Allen Brain Institute's stand-alone software package BrainExplorer.
+
+Terms of use
+The Scalable Brain Atlas does not "own" any of its templates. To ensure that the atlas makers receive proper credit, you must abide by our citation policy.
+In brief, always (1) cite each data source that contributed to your analysis, and (2) cite the Scalable Brain Atlas main publication and plugin references where appropriate.
+The defining citations for this atlas template are:
+Lein ES, Hawrylycz MJ, Ao N, et al. (2007) "Genome-wide atlas of gene expression in the adult mouse brain." Nature 445(7124):168-76. [doi 10.1038/nature05453]

input/C57BL6_mouse/DSURQE.note.txt

@@ -0,0 +1,40 @@
+The DSURQE atlas was nonlinear warpped to DSI Studio's C57BL/6 space
+
+
+source: http://repo.mouseimaging.ca/repo/DSURQE_40micron/notes_on_DSURQE_atlas
+Based on the following atlases:
+* Dorr et.al., 2008, High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice.
+* Steadman et.al., 2014, Genetic effects on cerebellar structure across mouse models of autism using a magnetic resonance imaging atlas.
+* Ullmann et.al., 2013, A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex.
+* Richards et.al, 2011, Segmentation of the mouse hippocampal formation in magnetic resonance images.
+* Shannon Egan (2015) – added olfactory bulb segmentation based on data from the Allen Brain Institute 
+* Lily Qiu (2016) – added the medial amygdala and medial preoptic area
+
+Compared to DSURE
+=================
+* added Medial amygdala (segmentated by Lily)
+* added Medial preoptic nucleus (segmented by Lily)
+--> these labels were mapped from the Dorr_2008 average (which was used for the segmentation) onto the 
+    40 micron average. The segmentation should be cleaned up at some point
+
+(DSURE atlas notes) Compared to DSUR
+====================================
+* olfactory layers segmented by Shannon Egan have been incorporated
+* all the old hippocampus labels (including the stratum granulosum and dentate gyrus) have been updated
+* voxels in the right side of the brain labeled as left have been fixed (same for the other way around)
+* spurious labeled voxels outside of the brain have been removed
+
+(DSUR atlas notes) Compared to DSU
+==================================
+* Fixes in the hippocampus have been made from slice 200-240(ish). What still needs to be done in terms of the hippocampus are slices 199-151. This also means that there are voxels labeled:
+
+label value, name
+6          , "TODO-fix-me-old hippocampus right"
+13         , "TODO-fix-me-old stratum granulosum of hippocampus right"
+16         , "TODO-fix-me-old dentate gyrus of hippocampus right"
+63         , "TODO-fix-me-old stratum granulosum of hippocampus left"
+66         , "TODO-fix-me-old dentate gyrus of hippocampus left"
+106        , "TODO-fix-me-old hippocampus left"
+
+* Fixes were made to the boundary of the cortex (outside of the brain, and around the corpus callosum). These were roughly made in slices 199-233
+

input/C57BL6_mouse/DSURQE.txt

@@ -0,0 +1,337 @@
+1	dentate_nucleus_right	255	0	0
+2	Label_2	0	255	0
+3	nucleus_interpositus_left	0	0	255
+4	thalamus_left	255	255	0
+5	olfactory_bulbs_right	0	255	255
+7	striatum_right	255	239	213
+8	corpus_callosum_right	0	0	205
+9	colliculus_superior_right	205	133	63
+10	periaqueductal_grey	210	180	140
+11	fimbria_left	102	205	170
+12	internal_capsule_left	0	0	128
+14	cerebral_peduncle_left	46	139	87
+15	fastigial_nucleus_right	255	228	225
+17	striatum_left	221	160	221
+18	corticospinal_tract/pyramids_left	233	150	122
+19	facial_nerve_(cranial_nerve_7)_right	165	42	42
+20	medial_lemniscus/medial_longitudinal_fasciculus_right	255	250	250
+21	anterior_lobule_white_matter_right	147	112	219
+22	fornix_left	218	112	214
+23	anterior_commissure_pars_posterior_right	75	0	130
+24	Cingulate_cortex_area_24a_right	255	182	193
+25	fasciculus_retroflexus_right	60	179	113
+26	Cingulate_cortex_area_24a'_right	255	235	205
+27	Cingulate_cortex_area_24b_right	255	228	196
+28	Cingulate_cortex_area_24b'_right	218	165	32
+29	Cingulate_cortex_area_25_right	0	128	128
+30	Cingulate_cortex_area_29a_right	188	143	143
+31	anterior_lobule_white_matter_left	255	105	180
+32	lobules_1-2_lingula_and_central_lobule_(ventral)_left	255	218	185
+33	lobule_3_white_matter_left	222	184	135
+34	lobules_4-5_culmen_(ventral_and_dorsal)_left	127	255	0
+35	Cingulate_cortex_area_29b_right	139	69	19
+36	lobule_6_declive_left	124	252	0
+37	Cingulate_cortex_area_29c_right	255	255	224
+38	lobule_8_pyramis_left	70	130	180
+39	Cingulate_cortex_area_30_right	0	100	0
+40	lobule_10_nodulus_left	238	130	238
+41	Cingulate_cortex_area_32_right	238	232	170
+42	Amygdalopiriform_transition_area_right	240	255	240
+43	colliculus_inferior_left	245	222	179
+44	globus_pallidus_right	184	134	11
+45	cerebellar_peduncle_middle_right	32	178	170
+46	Primary_auditory_cortex_right	255	20	147
+47	trunk_of_arbor_vita_left	25	25	112
+48	Secondary_auditory_cortex_dorsal_area_right	112	128	144
+49	Secondary_auditory_cortex_ventral_area_right	34	139	34
+50	Caudomedial_entorhinal_cortex_right	248	248	255
+51	amygdala_right	245	255	250
+52	basal_forebrain_right	255	160	122
+53	medial_septum_right	144	238	144
+54	fundus_of_striatum_right	173	255	47
+55	nucleus_accumbens_right	65	105	225
+56	Cingulum__right	255	99	71
+57	lateral_ventricle_right	150	40	130
+58	Claustrum_right	128	0	0
+59	stria_terminalis_right	50	205	50
+60	Cortex-amygdala_transition_zones_right	244	164	96
+61	mammillary_bodies_left	255	255	240
+62	Claustrum_dorsal_part_right	123	104	238
+65	Dorsal_nucleus_of_the_endopiriform_right	255	192	203
+67	Dorsal_intermediate_entorhinal_cortex_right	255	140	0
+68	corpus_callosum_left	143	188	143
+69	Dorsolateral_entorhinal_cortex_right	220	20	60
+70	Dorsolateral_orbital_cortex_right	253	245	230
+71	Dorsal_tenia_tecta_right	255	250	240
+72	Ectorhinal_cortex_right	0	206	209
+73	Frontal_cortex_area_3_right	0	255	127
+74	Frontal_association_cortex_right	128	0	128
+75	Intermediate_nucleus_of_the_endopiriform_claustrum_right	255	250	205
+76	bed_nucleus_of_stria_terminalis_left	250	128	114
+77	lateral_ventricle_left	148	0	211
+78	Insular_region_not_subdivided_right	178	34	34
+79	Lateral_orbital_cortex_right	255	127	80
+80	Lateral_parietal_association_cortex_right	135	206	235
+81	Primary_motor_cortex_right	100	149	237
+82	Secondary_motor_cortex_right	240	230	140
+83	Medial_entorhinal_cortex_right	250	235	215
+84	Medial_orbital_cortex_right	255	245	238
+85	pontine_nucleus_right	107	142	35
+86	Medial_parietal_association_cortex_right	135	206	250
+87	Piriform_cortex_right	0	0	139
+88	Posterolateral_cortical_amygdaloid_area__right	139	0	139
+89	Posteromedial_cortical_amygdaloid_area__right	245	245	220
+90	anterior_lobule__(lobules_4-5)_right	186	85	211
+91	simple_lobule_(lobule_6)_left	255	228	181
+92	crus_1_ansiform_lobule_(lobule_6)_right	255	222	173
+93	crus_2_ansiform_lobule_(lobule_7)_left	0	191	255
+94	paramedian_lobule_(lobule_7)_right	210	105	30
+95	olfactory_tubercle_right	255	248	220
+96	copula_pyramis_(lobule_8)_left	47	79	79
+97	flocculus_(FL)_right	72	61	139
+98	paraflocculus_(PFL)_left	175	238	238
+99	habenular_commissure_right	128	128	0
+100	posterior_commissure	176	224	230
+101	lateral_olfactory_tract_right	255	240	245
+102	lateral_olfactory_tract_left	139	0	0
+103	anterior_commissure_pars_posterior_left	240	255	255
+104	Perirhinal_cortex_right	255	215	0
+105	olfactory_bulbs_left	216	191	216
+107	lateral_septum_left	219	112	147
+108	Parietal_cortex_posterior_area_rostral_part_right	72	209	204
+109	colliculus_superior_left	255	0	255
+110	Rostral_amygdalopiriform_area_right	199	21	133
+111	Primary_somatosensory_cortex_right	154	205	50
+112	internal_capsule_right	189	183	107
+113	inferior_olivary_complex_right	240	248	255
+114	cerebral_peduncle_right	230	230	250
+115	anterior_commissure_pars_anterior_right	0	250	154
+116	optic_tract_left	85	107	47
+117	Primary_somatosensory_cortex_barrel_field_right	64	224	208
+118	fourth_ventricle	153	50	204
+119	cerebral_aqueduct	205	92	92
+120	medial_lemniscus/medial_longitudinal_fasciculus_left	250	250	210
+121	Primary_somatosensory_cortex_dysgranular_zone_right	95	158	160
+122	fornix_right	0	128	0
+123	cerebellar_peduncle_inferior_right	255	69	0
+124	superior_olivary_complex_right	224	255	255
+125	fasciculus_retroflexus_left	176	196	222
+126	Primary_somatosensory_cortex_forelimb_region_right	138	43	226
+127	Primary_somatosensory_cortex_hindlimb_region_right	30	144	255
+128	Primary_somatosensory_cortex_jaw_region_right	240	128	128
+129	Primary_somatosensory_cortex_shoulder_region_right	152	251	152
+131	pre-para_subiculum_left	255	0	0
+132	Primary_somatosensory_cortex_trunk_region_right	0	255	0
+133	pre-para_subiculum_right	0	0	255
+134	Primary_somatosensory_cortex_upper_lip_region_right	255	255	0
+135	Secondary_somatosensory_cortex_right	0	255	255
+136	Temporal_association_area_right	255	0	255
+137	Primary_visual_cortex_right	255	239	213
+138	Primary_visual_cortex_binocular_area_right	0	0	205
+139	lobule_9_white_matter_left	205	133	63
+140	subependymale_zone_/_rhinocele_left	210	180	140
+141	Primary_visual_cortex_monocular_area_right	102	205	170
+142	Secondary_visual_cortex_lateral_area_right	0	0	128
+143	colliculus_inferior_right	0	139	139
+144	globus_pallidus_left	46	139	87
+145	olfactory_tubercle_left	255	228	225
+146	third_ventricle	106	90	205
+147	Secondary_visual_cortex_mediolateral_area_right	221	160	221
+148	anterior_lobule__(lobules_4-5)_left	233	150	122
+149	Secondary_visual_cortex_mediomedial_area_right	165	42	42
+150	hypothalamus_left	255	250	250
+151	amygdala_left	147	112	219
+152	basal_forebrain_left	218	112	214
+153	medial_septum_left	75	0	130
+154	fundus_of_striatum_left	255	182	193
+155	nucleus_accumbens_left	60	179	113
+156	ventral_tegmental_decussation	255	235	205
+157	interpedunclar_nucleus	255	228	196
+158	Claustrum_ventral_part_right	218	165	32
+159	stria_terminalis_left	0	128	128
+160	Ventral_nucleus_of_the_endopiriform_claustrum_right	188	143	143
+161	mammillary_bodies_right	255	105	180
+162	Ventral_intermediate_entorhinal_cortex_right	255	218	185
+163	Ventral_orbital_cortex_right	222	184	135
+165	Ventral_tenia_tecta_right	139	69	19
+166	cuneate_nucleus_right	124	252	0
+167	flocculus_white_matter_right	255	255	224
+168	cuneate_nucleus_left	70	130	180
+169	Cingulate_cortex_area_24a_left	0	100	0
+170	crus_1_white_matter_left	238	130	238
+171	Cingulate_cortex_area_24a'_left	238	232	170
+172	Cingulate_cortex_area_24b_left	240	255	240
+173	Cingulate_cortex_area_24b'_left	245	222	179
+174	medulla	184	134	11
+175	trunk_of_crus_2_and_paramedian_white_matter_right	32	178	170
+176	bed_nucleus_of_stria_terminalis_right	255	20	147
+177	flocculus_white_matter_left	25	25	112
+178	Cingulate_cortex_area_25_left	112	128	144
+179	Cingulate_cortex_area_29a_left	34	139	34
+182	Cingulate_cortex_area_29b_left	255	160	122
+183	paraflocculus_white_matter_right	144	238	144
+184	Cingulate_cortex_area_29c_left	173	255	47
+185	pontine_nucleus_left	65	105	225
+186	Cingulate_cortex_area_30_left	255	99	71
+187	pons	250	240	230
+188	Cingulate_cortex_area_32_left	128	0	0
+189	Amygdalopiriform_transition_area_left	50	205	50
+191	simple_lobule_(lobule_6)_right	255	255	240
+192	crus_1_ansiform_lobule_(lobule_6)_left	123	104	238
+193	crus_2_ansiform_lobule_(lobule_7)_right	255	165	0
+194	midbrain	173	216	230
+195	trunk_of_crus_2_and_paramedian_white_matter_left	255	192	203
+196	copula_pyramis_(lobule_8)_right	127	255	212
+197	flocculus_(FL)_left	255	140	0
+198	paraflocculus_(PFL)_right	143	188	143
+199	habenular_commissure_left	220	20	60
+200	paramedian_lobule_(lobule_7)_left	253	245	230
+201	dentate_nucleus_left	255	250	240
+203	nucleus_interpositus_right	0	255	127
+204	thalamus_right	128	0	128
+205	stria_medullaris_left	255	250	205
+206	fastigial_nucleus_left	250	128	114
+207	lateral_septum_right	148	0	211
+208	Primary_auditory_cortex_left	178	34	34
+210	mammilothalamic_tract_right	135	206	235
+211	fimbria_right	100	149	237
+212	mammilothalamic_tract_left	240	230	140
+213	inferior_olivary_complex_left	250	235	215
+214	superior_olivary_complex_left	255	245	238
+215	anterior_commissure_pars_anterior_left	107	142	35
+216	optic_tract_right	135	206	250
+217	Secondary_auditory_cortex_dorsal_area_left	0	0	139
+218	corticospinal_tract/pyramids_right	139	0	139
+219	facial_nerve_(cranial_nerve_7)_left	245	245	220
+220	crus_1_white_matter_right	186	85	211
+221	Secondary_auditory_cortex_ventral_area_left	255	228	181
+222	cerebellar_peduncle_superior_left	255	222	173
+223	cerebellar_peduncle_inferior_left	0	191	255
+224	copula_white_matter_right	210	105	30
+225	stria_medullaris_right	255	248	220
+226	trunk_of_simple_and_crus_1_white_matter_right	47	79	79
+227	Caudomedial_entorhinal_cortex_left	72	61	139
+228	paramedian_lobule_right	175	238	238
+229	crus_2_white_matter_right	128	128	0
+231	Cingulum__left	255	240	245
+232	lobule_1-2_white_matter_left	139	0	0
+233	lobule_3_central_lobule_(dorsal)_left	240	255	255
+234	lobules_4-5_white_matter_left	255	215	0
+235	Claustrum_left	216	191	216
+236	lobules_6-7_white_matter_left	119	136	153
+237	lobule_7_tuber_(or_folium)_left	219	112	147
+238	lobule_8_white_matter_left	72	209	204
+239	lobule_9_uvula_left	255	0	255
+240	subependymale_zone_/_rhinocele_right	199	21	133
+241	simple_lobule_white_matter_right	154	205	50
+242	cerebellar_peduncle_superior_right	189	183	107
+243	paraflocculus_white_matter_left	240	248	255
+244	copula_white_matter_left	230	230	250
+245	cerebellar_peduncle_middle_left	0	250	154
+246	trunk_of_simple_and_crus_1_white_matter_left	85	107	47
+248	paramedian_lobule_left	153	50	204
+249	crus_2_white_matter_left	205	92	92
+250	hypothalamus_right	250	250	210
+251	simple_lobule_white_matter_left	95	158	160
+252	lobule_10_white_matter_left	0	128	0
+253	trunk_of_lobules_1-3_white_matter_left	255	69	0
+254	trunk_of_lobules_6-8_white_matter_left	224	255	255
+255	Cortex-amygdala_transition_zones_left	176	196	222
+256	Claustrum_dorsal_part_left	138	43	226
+257	Dorsal_nucleus_of_the_endopiriform_left	30	144	255
+258	Dorsal_intermediate_entorhinal_cortex_left	240	128	128
+259	Dorsolateral_entorhinal_cortex_left	152	251	152
+260	Dorsolateral_orbital_cortex_left	160	82	45
+261	Dorsal_tenia_tecta_left	255	0	0
+262	Ectorhinal_cortex_left	0	255	0
+263	Frontal_cortex_area_3_left	0	0	255
+264	Frontal_association_cortex_left	255	255	0
+265	Intermediate_nucleus_of_the_endopiriform_claustrum_left	0	255	255
+266	Insular_region_not_subdivided_left	255	0	255
+267	Lateral_orbital_cortex_left	255	239	213
+268	Lateral_parietal_association_cortex_left	0	0	205
+269	Primary_motor_cortex_left	205	133	63
+270	Secondary_motor_cortex_left	210	180	140
+271	Medial_entorhinal_cortex_left	102	205	170
+272	Medial_orbital_cortex_left	0	0	128
+273	Medial_parietal_association_cortex_left	0	139	139
+274	Piriform_cortex_left	46	139	87
+275	Posterolateral_cortical_amygdaloid_area__left	255	228	225
+276	Posteromedial_cortical_amygdaloid_area__left	106	90	205
+277	Perirhinal_cortex_left	221	160	221
+278	Parietal_cortex_posterior_area_rostral_part_left	233	150	122
+279	Rostral_amygdalopiriform_area_left	165	42	42
+280	Primary_somatosensory_cortex_left	255	250	250
+281	Primary_somatosensory_cortex_barrel_field_left	147	112	219
+282	Primary_somatosensory_cortex_dysgranular_zone_left	218	112	214
+283	Primary_somatosensory_cortex_forelimb_region_left	75	0	130
+284	Primary_somatosensory_cortex_hindlimb_region_left	255	182	193
+285	Primary_somatosensory_cortex_jaw_region_left	60	179	113
+286	Primary_somatosensory_cortex_shoulder_region_left	255	235	205
+287	Primary_somatosensory_cortex_trunk_region_left	255	228	196
+288	Primary_somatosensory_cortex_upper_lip_region_left	218	165	32
+289	Secondary_somatosensory_cortex_left	0	128	128
+290	Temporal_association_area_left	188	143	143
+291	Primary_visual_cortex_left	255	105	180
+292	Primary_visual_cortex_binocular_area_left	255	218	185
+293	Primary_visual_cortex_monocular_area_left	222	184	135
+294	Secondary_visual_cortex_lateral_area_left	127	255	0
+295	Secondary_visual_cortex_mediolateral_area_left	139	69	19
+296	Secondary_visual_cortex_mediomedial_area_left	124	252	0
+297	Claustrum_ventral_part_left	255	255	224
+298	Ventral_nucleus_of_the_endopiriform_claustrum_left	70	130	180
+299	Ventral_intermediate_entorhinal_cortex_left	0	100	0
+300	Ventral_orbital_cortex_left	238	130	238
+301	Ventral_tenia_tecta_left	238	232	170
+305	CA1Or_left	32	178	170
+306	LMol_right	255	20	147
+307	LMol_left	25	25	112
+308	CA1Rad_right	112	128	144
+309	CA1Rad_left	34	139	34
+310	CA2Py_right	248	248	60
+311	CA2Py_left	245	255	60
+312	CA2Or_right	255	160	22
+313	CA2Or_left	144	238	144
+314	CA2Rad_right	173	255	47
+315	CA2Rad_left	65	105	225
+316	CA3Py_Inner_right	255	99	71
+317	CA3Py_Inner_left	150	123	11
+318	CA3Py_Outer_right	128	0	0
+319	CA3Py_Outer_left	50	205	50
+320	CA3Or_right	244	164	96
+321	CA3Or_left	255	255	240
+322	CA3Rad_right	123	104	238
+323	CA3Rad_left	255	165	0
+324	SLu_right	173	216	230
+325	SLu_left	255	192	203
+326	MoDG_right	127	255	212
+327	MoDG_left	255	140	0
+328	GrDG_right	143	188	143
+329	GrDG_left	220	20	60
+330	PoDG_right	253	245	230
+331	PoDG_left	255	250	240
+332	Subiculum_right	255	60	154
+333	Subiculum_left	185	85	195
+334	CA1Py_right	240	255	240
+335	CA1Py_left	245	222	179
+336	CA1Or_right	184	134	11
+337	Olfactory_bulb_glomerular_layer_right	148	0	211
+338	Olfactory_bulb_external_plexiform_layer_right	178	34	34
+339	Olfactory_bulb_mitral_cell_layer_right	255	127	80
+340	Olfactory_bulb_internal_plexiform_layer_right	135	206	235
+341	Olfactory_bulb_granule_cell_layer_right	100	149	237
+342	Accessory_olfactory_bulb_glomerular,_external_plexiform_and_mitral_cell_layer_right	240	230	140
+343	Accessory_olfactory_bulb_granule_cell_layer_right	250	235	215
+344	Anterior_olfactory_nucleus_right	255	245	238
+345	Olfactory_bulb_glomerular_layer_left	107	142	35
+346	Olfactory_bulb_external_plexiform_layer_left	135	206	250
+347	Olfactory_bulb_mitral_cell_layer_left	0	0	139
+348	Olfactory_bulb_internal_plexiform_layer_left	139	0	139
+349	Olfactory_bulb_granule_cell_layer_left	245	245	220
+350	Accessory_olfactory_bulb_glomerular,_external_plexiform_and_mitral_cell_layer_left	186	85	211
+351	Accessory_olfactory_bulb_granule_cell_layer_left	255	228	181
+352	Anterior_olfactory_nucleus_left	255	222	173
+353	Medial_amygdala_right	0	191	255
+354	Medial_preoptic_nucleus_right	210	105	30
+355	Medial_amygdala_left	255	248	220
+356	Medial_preoptic_nucleus_left	47	79	79

input/C57BL6_mouse/DukeRCCF.license.txt

@@ -0,0 +1,15 @@
+Reference:
+
+HiDiver: A Suite of Methods to Merge Magnetic Resonance Histology, Light Sheet Microscopy, and Complete Brain Delineations
+G. Allan Johnson, Yuqi Tian, Gary P. Cofer, James C. Cook, James C. Gee, Adam Hall,  View ORCID ProfileKathryn Hornburg, Yi Qi, Fang-Cheng Yeh, Nian Wang, Leonard E. White, Robert W. Williams
+doi: https://doi.org/10.1101/2022.02.10.479607
+
+
+
+1. These data are made available as a service to the research community by Duke University through its Center for In Vivo Microscopy ("Duke CIVM"), located at DUMC-Center for InVivo Microscopy, Bryan Research Building, 311 Research Dr, Box 3302, Durham, NC 27710.
+
+2.The data are provided for research and educational uses. No rights are provided to User under any patent applications, trade secrets, copyrights, or other proprietary rights of Duke CIVM, except as necessary to use the data and images for such research and educational purposes. Neither this data nor the results of use of the data shall be used as the basis for any commercial product or service offered to third parties
+
+3. The user shall not transfer the data and images contained herein to any third party. The User shall not rebroadcast or publicly display images or video without express written permission from Duke CIVM. This shall not be taken to prevent the User from including representative images and data in academic publications of User's research results.
+
+4. The User is encouraged to publish the results of his or her research. All publications based upon use of the data shall acknowledge the Duke University Center for In Vivo Microscopy and Calabrese et al Cerebral Cortex 25(11), pp 4628-4637, 2015.

input/C57BL6_mouse/DukeRCCF.txt

@@ -0,0 +1,360 @@
+1 CH__Cerebrum_left
+2 grey__Basic_cell_groups_and_regions_left
+3 OB__Olfactory_bulb_left
+4 AON__Anterior_olfactory_nucleus_left
+5 FRP__Frontal_pole__cerebral_cortex_left
+6 ORB__Orbital_area_left
+7 PL__Prelimbic_area_left
+8 ILA__Infralimbic_area_left
+9 ACA__Anterior_cingulate_area_left
+10 AI__Agranular_insular_area_left
+11 GU__Gustatory_areas_left
+12 PIR__Piriform_area_left
+13 VISC__Visceral_area_left
+14 MOp__Primary_motor_area_left
+15 MOs__Secondary_motor_area_left
+16 SSp__Primary_somatosensory_area_left
+17 SSp-bfd__Primary_somatosensory_area__barrel_field_left
+18 SSs__Supplemental_somatosensory_area_left
+19 PTLp__Posterior_parietal_association_areas_left
+20 AUD__Auditory_areas_left
+21 TEa__Temporal_association_areas_left
+22 ECT__Ectorhinal_area_left
+23 PERI__Perirhinal_area_left
+24 RSP__Retrosplenial_area_left
+25 VIS__Visual_areas_left
+26 VISp__Primary_visual_area_left
+27 ENT__Entorhinal_area_left
+28 SUBR__Subicular_region_left
+29 HI__Hippocampus_left
+30 HIP__Hippocampal_region_left
+31 CA1__Field_CA1_left
+32 CA3__Field_CA3_left
+33 DG__Dentate_gyrus_left
+34 DG-sg__Dentate_gyrus__granule_cell_layer_left
+35 DG-po__Dentate_gyrus__polymorph_layer_left
+36 CLA__Claustrum_left
+37 CEA__Central_amygdalar_nucleus_left
+38 sAMY__Striatum-like_amygdalar_nuclei_left
+39 MEA__Medial_amygdalar_nucleus_left
+40 LA__Lateral_amygdalar_nucleus_left
+41 BLA__Basolateral_amygdalar_nucleus_left
+42 BMA__Basomedial_amygdalar_nucleus_left
+43 PA__Posterior_amygdalar_nucleus_left
+44 COAz__Cortical_amygdalar_zones_left
+45 EP__Endopiriform_nucleus_left
+46 STR__Striatum_left
+47 STRd__Striatum_dorsal_region_left
+48 ACB__Nucleus_accumbens_left
+49 FS__Fundus_of_striatum_left
+50 OT__Olfactory_tubercle_left
+51 GPe__Globus_pallidus__external_segment_left
+52 GPi__Globus_pallidus__internal_segment_left
+53 SI__Substantia_innominata_left
+54 MSC__Medial_septal_complex_left
+55 LS__Lateral_septal_nucleus_left
+56 BST__Bed_nuclei_of_the_stria_terminalis_left
+57 MA__Magnocellular_nucleus__Meynert__left
+58 TH__Thalamus_left
+59 AM__Anteromedial_nucleus_left
+60 AD__Anterodorsal_nucleus_left
+61 AV__Anteroventral_nucleus_of_thalamus_left
+62 LD__Lateral_dorsal_nucleus_of_the_thalamus_left
+63 VAL__Ventral_anterior-lateral_complex_of_the_thalamus_left
+64 VM__Ventral_medial_nucleus_of_the_thalamus_left
+65 VP__Ventral_posterior_complex_of_the_thalamus_left
+66 VPM__Ventral_posteromedial_nucleus_of_the_thalamus_left
+67 VPL__Ventral_posterolateral_nucleus_of_the_thalamus_left
+68 PT__Parataenial_nucleus_left
+69 PVT__Paraventricular_nucleus_of_the_thalamus_left
+70 RE__Nucleus_of_reuniens_left
+71 CL__Central_lateral_nucleus_of_the_thalamus_left
+72 CM__Central_medial_nucleus_of_the_thalamus_left
+73 PCN__Paracentral_nucleus_left
+74 PF__Parafascicular_nucleus_left
+75 PIL__Posterior_intralaminar_thalamic_nucleus_left
+76 MD__Mediodorsal_nucleus_of_thalamus_left
+77 LP__Lateral_posterior_nucleus_of_the_thalamus_left
+78 PO__Posterior_complex_of_the_thalamus_left
+79 MGd__Medial_geniculate_complex__dorsal_part_left
+80 MGv__Medial_geniculate_complex__ventral_part_left
+81 MGm__Medial_geniculate_complex__medial_part_left
+82 LGd__Dorsal_part_of_the_lateral_geniculate_complex_left
+83 LGv__Ventral_part_of_the_lateral_geniculate_complex_left
+84 RT__Reticular_nucleus_of_the_thalamus_left
+85 LH__Lateral_habenula_left
+86 MH__Medial_habenula_left
+87 HY__Hypothalamus_left
+88 MPN__Medial_preoptic_nucleus_left
+89 AHN__Anterior_hypothalamic_nucleus_left
+90 VMH__Ventromedial_hypothalamic_nucleus_left
+91 PH__Posterior_hypothalamic_nucleus_left
+92 MBO__Mammillary_body_left
+93 SCH__Suprachiasmatic_nucleus_left
+94 ARH__Arcuate_hypothalamic_nucleus_left
+95 PVH__Paraventricular_hypothalamic_nucleus_left
+96 LPO__Lateral_preoptic_area_left
+97 TU__Tuberal_nucleus_left
+98 LHA__Lateral_hypothalamic_area_left
+99 STN__Subthalamic_nucleus_left
+100 ZI__Zona_incerta_left
+101 SCs__Superior_colliculus__sensory_related_left
+102 SCm__Superior_colliculus__motor_related_left
+103 IC__Inferior_colliculus_left
+104 ICc__Inferior_colliculus__central_nucleus_left
+105 PBG__Parabigeminal_nucleus_left
+106 PPN__Pedunculopontine_nucleus_left
+107 PRT__Pretectal_region_left
+108 IIIR__Oculomotor_region_left
+109 PAG__Periaqueductal_gray_left
+110 RN__Red_nucleus_left
+111 MRN__Midbrain_reticular_nucleus_left
+112 CUN__Cuneiform_nucleus_left
+113 IPN__Interpeduncular_nucleus_left
+114 VTA__Ventral_tegmental_area_left
+115 SNc__Substantia_nigra__compact_part_left
+116 SNr__Substantia_nigra__reticular_part_left
+117 DR__Dorsal_nucleus_raphe_left
+118 P__Pons_left
+119 NLL__Nucleus_of_the_lateral_lemniscus_left
+120 SOC__Superior_olivary_complex_left
+121 PB__Parabrachial_nucleus_left
+122 PSV__Principal_sensory_nucleus_of_the_trigeminal_left
+123 PCG__Pontine_central_gray_left
+124 PG__Pontine_gray_left
+125 VMc__Trigeminal_motor_complex_left
+126 VII__Facial_motor_nucleus_left
+127 DTN__Dorsal_tegmental_nucleus_left
+128 LDT__Laterodorsal_tegmental_nucleus_left
+129 TRN__Tegmental_reticular_nucleus_left
+130 PRF__Pontine_reticular_formation_left
+131 RVC__Raphe_ventral_complex_left
+132 HEM__Hemispheric_regions_left
+133 VERM__Vermal_regions_left
+134 PFL__Paraflocculus_left
+135 FLNOD__Floccular_nodular_region_left
+136 DN__Dentate_nucleus_left
+137 IP__Interposed_nucleus_left
+138 FN__Fastigial_nucleus_left
+139 VeCB__Vestibulocerebellar_nucleus_left
+140 NTB__Nucleus_of_the_trapezoid_body_left
+141 SPVr__Spinal_nucleus_of_the_trigeminal_region_left
+142 NTS__Nucleus_of_the_solitary_tract_left
+143 DCO__Dorsal_cochlear_nucleus_left
+144 VCO__Ventral_cochlear_nucleus_left
+145 VNC__Vestibular_nuclei_left
+146 SPIV__Spinal_vestibular_nucleus_left
+147 DCN__Dorsal_column_nuclei_left
+148 IO__Inferior_olivary_complex_left
+149 PHY__Perihypoglossal_nuclei_left
+150 DMX__Dorsal_motor_nucleus_of_the_vagus_nerve_left
+151 XII__Hypoglossal_nucleus_left
+152 MRz__Medullary_reticular_zone_left
+153 IRN__Intermediate_reticular_nucleus_left
+154 MY-sat__Medulla__raphe__behavioral_state_related_left
+155 fiber_tracts__fiber_tracts_left
+156 cc__corpus_callosum_left
+157 cing__cingulum_bundle_left
+158 ac__anterior_commissure_left
+159 optc__optic_tract_and_chiasm_left
+160 dhc__dorsal_hippocampal_commissure_left
+161 fi__fimbria_left
+162 fx__columns_of_the_fornix_left
+163 st__stria_terminalis_left
+164 lfbst__thalamus_related_left
+165 mfb__medial_forebrain_bundle_left
+166 fr__fasciculus_retroflexus_left
+167 pc__posterior_commissure_left
+168 cst__corticospinal_tract_left
+169 ml__medial_lemniscus_left
+170 ll__lateral_lemniscus_left
+171 mlf__medial_longitudinal_fascicle_left
+172 scp__superior_cerebelar_peduncles_left
+173 icp__inferior_cerebellar_peduncle_left
+174 Vn__Trigeminal_nerve_left
+175 cVIIIn__cochlear_nerve_left
+176 VL__lateral_ventricle_left
+177 V3__third_ventricle_left
+178 V4__fourth_ventricle_left
+179 AQ__cerebral_aqueduct_left
+180 Brain__Whole_brain__root__left
+1001 CH__Cerebrum_right
+1002 grey__Basic_cell_groups_and_regions_right
+1003 OB__Olfactory_bulb_right
+1004 AON__Anterior_olfactory_nucleus_right
+1005 FRP__Frontal_pole__cerebral_cortex_right
+1006 ORB__Orbital_area_right
+1007 PL__Prelimbic_area_right
+1008 ILA__Infralimbic_area_right
+1009 ACA__Anterior_cingulate_area_right
+1010 AI__Agranular_insular_area_right
+1011 GU__Gustatory_areas_right
+1012 PIR__Piriform_area_right
+1013 VISC__Visceral_area_right
+1014 MOp__Primary_motor_area_right
+1015 MOs__Secondary_motor_area_right
+1016 SSp__Primary_somatosensory_area_right
+1017 SSp-bfd__Primary_somatosensory_area__barrel_field_right
+1018 SSs__Supplemental_somatosensory_area_right
+1019 PTLp__Posterior_parietal_association_areas_right
+1020 AUD__Auditory_areas_right
+1021 TEa__Temporal_association_areas_right
+1022 ECT__Ectorhinal_area_right
+1023 PERI__Perirhinal_area_right
+1024 RSP__Retrosplenial_area_right
+1025 VIS__Visual_areas_right
+1026 VISp__Primary_visual_area_right
+1027 ENT__Entorhinal_area_right
+1028 SUBR__Subicular_region_right
+1029 HI__Hippocampus_right
+1030 HIP__Hippocampal_region_right
+1031 CA1__Field_CA1_right
+1032 CA3__Field_CA3_right
+1033 DG__Dentate_gyrus_right
+1034 DG-sg__Dentate_gyrus__granule_cell_layer_right
+1035 DG-po__Dentate_gyrus__polymorph_layer_right
+1036 CLA__Claustrum_right
+1037 CEA__Central_amygdalar_nucleus_right
+1038 sAMY__Striatum-like_amygdalar_nuclei_right
+1039 MEA__Medial_amygdalar_nucleus_right
+1040 LA__Lateral_amygdalar_nucleus_right
+1041 BLA__Basolateral_amygdalar_nucleus_right
+1042 BMA__Basomedial_amygdalar_nucleus_right
+1043 PA__Posterior_amygdalar_nucleus_right
+1044 COAz__Cortical_amygdalar_zones_right
+1045 EP__Endopiriform_nucleus_right
+1046 STR__Striatum_right
+1047 STRd__Striatum_dorsal_region_right
+1048 ACB__Nucleus_accumbens_right
+1049 FS__Fundus_of_striatum_right
+1050 OT__Olfactory_tubercle_right
+1051 GPe__Globus_pallidus__external_segment_right
+1052 GPi__Globus_pallidus__internal_segment_right
+1053 SI__Substantia_innominata_right
+1054 MSC__Medial_septal_complex_right
+1055 LS__Lateral_septal_nucleus_right
+1056 BST__Bed_nuclei_of_the_stria_terminalis_right
+1057 MA__Magnocellular_nucleus__Meynert__right
+1058 TH__Thalamus_right
+1059 AM__Anteromedial_nucleus_right
+1060 AD__Anterodorsal_nucleus_right
+1061 AV__Anteroventral_nucleus_of_thalamus_right
+1062 LD__Lateral_dorsal_nucleus_of_the_thalamus_right
+1063 VAL__Ventral_anterior-lateral_complex_of_the_thalamus_right
+1064 VM__Ventral_medial_nucleus_of_the_thalamus_right
+1065 VP__Ventral_posterior_complex_of_the_thalamus_right
+1066 VPM__Ventral_posteromedial_nucleus_of_the_thalamus_right
+1067 VPL__Ventral_posterolateral_nucleus_of_the_thalamus_right
+1068 PT__Parataenial_nucleus_right
+1069 PVT__Paraventricular_nucleus_of_the_thalamus_right
+1070 RE__Nucleus_of_reuniens_right
+1071 CL__Central_lateral_nucleus_of_the_thalamus_right
+1072 CM__Central_medial_nucleus_of_the_thalamus_right
+1073 PCN__Paracentral_nucleus_right
+1074 PF__Parafascicular_nucleus_right
+1075 PIL__Posterior_intralaminar_thalamic_nucleus_right
+1076 MD__Mediodorsal_nucleus_of_thalamus_right
+1077 LP__Lateral_posterior_nucleus_of_the_thalamus_right
+1078 PO__Posterior_complex_of_the_thalamus_right
+1079 MGd__Medial_geniculate_complex__dorsal_part_right
+1080 MGv__Medial_geniculate_complex__ventral_part_right
+1081 MGm__Medial_geniculate_complex__medial_part_right
+1082 LGd__Dorsal_part_of_the_lateral_geniculate_complex_right
+1083 LGv__Ventral_part_of_the_lateral_geniculate_complex_right
+1084 RT__Reticular_nucleus_of_the_thalamus_right
+1085 LH__Lateral_habenula_right
+1086 MH__Medial_habenula_right
+1087 HY__Hypothalamus_right
+1088 MPN__Medial_preoptic_nucleus_right
+1089 AHN__Anterior_hypothalamic_nucleus_right
+1090 VMH__Ventromedial_hypothalamic_nucleus_right
+1091 PH__Posterior_hypothalamic_nucleus_right
+1092 MBO__Mammillary_body_right
+1093 SCH__Suprachiasmatic_nucleus_right
+1094 ARH__Arcuate_hypothalamic_nucleus_right
+1095 PVH__Paraventricular_hypothalamic_nucleus_right
+1096 LPO__Lateral_preoptic_area_right
+1097 TU__Tuberal_nucleus_right
+1098 LHA__Lateral_hypothalamic_area_right
+1099 STN__Subthalamic_nucleus_right
+1100 ZI__Zona_incerta_right
+1101 SCs__Superior_colliculus__sensory_related_right
+1102 SCm__Superior_colliculus__motor_related_right
+1103 IC__Inferior_colliculus_right
+1104 ICc__Inferior_colliculus__central_nucleus_right
+1105 PBG__Parabigeminal_nucleus_right
+1106 PPN__Pedunculopontine_nucleus_right
+1107 PRT__Pretectal_region_right
+1108 IIIR__Oculomotor_region_right
+1109 PAG__Periaqueductal_gray_right
+1110 RN__Red_nucleus_right
+1111 MRN__Midbrain_reticular_nucleus_right
+1112 CUN__Cuneiform_nucleus_right
+1113 IPN__Interpeduncular_nucleus_right
+1114 VTA__Ventral_tegmental_area_right
+1115 SNc__Substantia_nigra__compact_part_right
+1116 SNr__Substantia_nigra__reticular_part_right
+1117 DR__Dorsal_nucleus_raphe_right
+1118 P__Pons_right
+1119 NLL__Nucleus_of_the_lateral_lemniscus_right
+1120 SOC__Superior_olivary_complex_right
+1121 PB__Parabrachial_nucleus_right
+1122 PSV__Principal_sensory_nucleus_of_the_trigeminal_right
+1123 PCG__Pontine_central_gray_right
+1124 PG__Pontine_gray_right
+1125 VMc__Trigeminal_motor_complex_right
+1126 VII__Facial_motor_nucleus_right
+1127 DTN__Dorsal_tegmental_nucleus_right
+1128 LDT__Laterodorsal_tegmental_nucleus_right
+1129 TRN__Tegmental_reticular_nucleus_right
+1130 PRF__Pontine_reticular_formation_right
+1131 RVC__Raphe_ventral_complex_right
+1132 HEM__Hemispheric_regions_right
+1133 VERM__Vermal_regions_right
+1134 PFL__Paraflocculus_right
+1135 FLNOD__Floccular_nodular_region_right
+1136 DN__Dentate_nucleus_right
+1137 IP__Interposed_nucleus_right
+1138 FN__Fastigial_nucleus_right
+1139 VeCB__Vestibulocerebellar_nucleus_right
+1140 NTB__Nucleus_of_the_trapezoid_body_right
+1141 SPVr__Spinal_nucleus_of_the_trigeminal_region_right
+1142 NTS__Nucleus_of_the_solitary_tract_right
+1143 DCO__Dorsal_cochlear_nucleus_right
+1144 VCO__Ventral_cochlear_nucleus_right
+1145 VNC__Vestibular_nuclei_right
+1146 SPIV__Spinal_vestibular_nucleus_right
+1147 DCN__Dorsal_column_nuclei_right
+1148 IO__Inferior_olivary_complex_right
+1149 PHY__Perihypoglossal_nuclei_right
+1150 DMX__Dorsal_motor_nucleus_of_the_vagus_nerve_right
+1151 XII__Hypoglossal_nucleus_right
+1152 MRz__Medullary_reticular_zone_right
+1153 IRN__Intermediate_reticular_nucleus_right
+1154 MY-sat__Medulla__raphe__behavioral_state_related_right
+1155 fiber_tracts__fiber_tracts_right
+1156 cc__corpus_callosum_right
+1157 cing__cingulum_bundle_right
+1158 ac__anterior_commissure_right
+1159 optc__optic_tract_and_chiasm_right
+1160 dhc__dorsal_hippocampal_commissure_right
+1161 fi__fimbria_right
+1162 fx__columns_of_the_fornix_right
+1163 st__stria_terminalis_right
+1164 lfbst__thalamus_related_right
+1165 mfb__medial_forebrain_bundle_right
+1166 fr__fasciculus_retroflexus_right
+1167 pc__posterior_commissure_right
+1168 cst__corticospinal_tract_right
+1169 ml__medial_lemniscus_right
+1170 ll__lateral_lemniscus_right
+1171 mlf__medial_longitudinal_fascicle_right
+1172 scp__superior_cerebelar_peduncles_right
+1173 icp__inferior_cerebellar_peduncle_right
+1174 Vn__Trigeminal_nerve_right
+1175 cVIIIn__cochlear_nerve_right
+1176 VL__lateral_ventricle_right
+1177 V3__third_ventricle_right
+1178 V4__fourth_ventricle_right
+1179 AQ__cerebral_aqueduct_right
+1180 Brain__Whole_brain__root__right

input/README.md

@@ -0,0 +1,5 @@
+# Inputs
+
+- **C57BL6_mouse folder**: The corresponding atlas folder from DSI Studio. This folder can also be found in the root directory where DSI Studio is installed.
+- **C57BL6_mouse_iso.nii.gz**: This is the iso NIFTI file created by loading the fib file from the C57BL6_mouse folder and saving the iso part of it as a NIFTI file. This file is equivalent to the C57BL6_mouse.ISO.nii.gz file in the C57BL6_mouse folder, which has a higher resolution. However, since the masks were drawn using the C57BL6_mouse.fib.gz file, this was saved separately.
+- **NP_template_sc0.nii.gz**: This is our in-house MRI template, also known as MTPL. Reference link to the paper: [Frontiers in Neuroinformatics](https://www.frontiersin.org/articles/10.3389/fninf.2019.00042/full), and the GitHub repository: [Aswendt-Lab/AIDAmri - SND_Mask_trafu branch](https://github.com/Aswendt-Lab/AIDAmri/blob/SND_Mask_trafu/lib/NP_template_sc0.nii.gz).

output/README.md

@@ -0,0 +1,6 @@
+# Outputs
+
+- **Nifti_Trakte**: Contains all manually drawn masks created with DSI Studio.
+- **Nifti_Trakte_registered**: Contains the masks registered to our in-house MRI template (MTPL). This registration was performed manually using `reg_aladin` and `reg_resample`.
+- **affineTrafo.txt**: This is the output transformation matrix generated by `reg_aladin` during the registration of the `C57BL6_mouse.iso.nii.gz` file to the `NP_template_sc0.nii.gz`.
+- **C57BL6_mouse.iso_registered.nii.gz**: This is the output image created by `reg_aladin` when registering the `C57BL6_mouse.iso.nii.gz` file to the `NP_template_sc0.nii.gz`.

output/affineTrafo.txt

@@ -0,0 +1,4 @@
+0.9781612 -0.0005830705 0.006048193 -0.02098001
+0.004167608 0.04551842 1.067904 -4.135002
+-0.005957384 -0.8691303 0.06396494 -1.328074
+0 0 0 1