This readme file was generated on [2023-12-06] by [Philippa J Johnson] GENERAL INFORMATION Title of Dataset: White Matter Atlas of the Domestic Canine Brain Author/Principal Investigator Information Name: Philippa J. Johnson ORCID:0000-0002-4558-0745 Institution: Cornell College of Veterinary Medicine, Department of Clinical Sciences Address: Cornell University, Ithaca, NY 14853, USA Email: pjj43@cornell.edu Author/Associate or Co-investigator Information Name: Fiona Inglis ORCID: Institution: Cornell College of Veterinary Medicine, Department of Clinical Sciences Address: Cornell University, Ithaca, NY 14853, USA Email: Fiona.Inglis@bluepearlvet.com Author/Alternate Contact Information Name: Paul Taylor ORCID: Institution: Scientific and Statistical Computing Core Address: National Institute of Mental Health, USA Email: ptaylor.afni@gmail.com Date of data collection: 6/11/2018 - 3/13/2019 Geographic location of data collection: Cornell Magnetic Resonance Imaging Center, Department of Human Ecology, Cornell University. Information about funding sources that supported the collection of the data: NA SHARING/ACCESS INFORMATION Licenses/restrictions placed on the data: None Links to publications that cite or use the data: TBD Links to other publicly accessible locations of the data: https://afni.nimh.nih.gov/ Links/relationships to ancillary data sets: This atlas corroborates to the cortical atlas created by Johnson et al (2020) Stereotactic Cortical Atlas of the Domestic Canine Brain. Sci Rep. 2020 Mar 16;10(1):4781. doi: 10.1038/s41598-020-61665-0 and Johnson, Philippa J, & Barry, Erica F. (2020). Cortical Atlas of the Canine Brain [Dataset]. Cornell University Library eCommons Repository. https://doi.org/10.7298/4T8Z-AW34.2 Was data derived from another source? No Recommended citation for this dataset: TBD DATA & FILE OVERVIEW File List: Cortical and Subcortical Atlas Files: corndog_v3_wm_atlas_manual.nii - Atlas of the subcortex generated from manual delineation of white matter regions corndog_v3_atlas_cort.nii - Atlas of the cortex generated from myeloarchitectonic boundaries corndog_v3_atlas_cort+subcort_RH.nii - Atlas of the cortex and subcortex of the right hemisphere corndog_v3_atlas_cort+subcort_LH.nii - Atlas of the cortex and subcortex of the left hemisphere corndog_v3_atlas_cort+subcort.nii - Atlas of the cortex and sub cortex of the whole brain Cortical Lobar Files: corndog_v3_lobe_mask_cingulate.nii.gz - mask depicting the cingulate region of the brain corndog_v3_lobe_mask_frontal.nii.gz - mask depicting the frontal region of the brain corndog_v3_lobe_mask_occipital.nii.gz - mask depicting the occipital region of the brain corndog_v3_lobe_mask_parietal.nii.gz - mask depicting the parietal region of the brain corndog_v3_lobe_mask_perisylvian.nii.gz - mask depicting the perisylvian region of the brain corndog_v3_lobe_mask_sensorymotor.nii.gz - mask depicting the sensorimotor region of the brain corndog_v3_lobe_mask_subcortical.nii.gz - mask depicting the entire subcortical region of the brain and is generating by summing all of the manual white matter priors corndog_v3_atlas_cort_LH.nii.gz - mask of the cortex of the left hemisphere corndog_v3_atlas_cort_RH.nii.gz - mask of the cortex of the right hemisphere Population Template Files: corndog_v3_template.nii.gz - Population average template generated from T1-weighted data corndog_v3_wm_V1.nii.gz - Population average template generated from DTI data corndog_v3_wm_FA.nii.gz - Population average template generated from DTI data corndog_v3_mask.nii.gz - Population average template generated from DTI data Label files label_file_corndog_v3_atlas_WM.txt - text file identifying the labels of the white matter atlas label_file_corndog_v3_atlas.txt - text file identifying the labels of the cortical atlas White matter tract files - All generated from virtual TrackVis dissection of a population average tractogram created from DTI data. wm = white matter, tr = track, Proj = projection, comm = commissural, cereb = cerebellar, assoc = association, olfac = olfactory, rh = right hemisphere, lh = left hemisphere. corndog_v3_wm_tr_proj_rh_Thalamic_Radiation.nii.gz corndog_v3_wm_tr_proj_rh_Optic_Radiation.nii.gz corndog_v3_wm_tr_proj_rh_Optic.nii.gz corndog_v3_wm_tr_proj_rh_Corticospinal.nii.gz corndog_v3_wm_tr_proj_lh_Thalamic_Radiation.nii.gz corndog_v3_wm_tr_proj_lh_Optic_Radiation.nii.gz corndog_v3_wm_tr_proj_lh_Optic.nii.gz corndog_v3_wm_tr_proj_lh_Corticospinal.nii.gz corndog_v3_wm_tr_proj_Fornix.nii.gz corndog_v3_wm_tr_comm_Tapetum.nii.gz corndog_v3_wm_tr_comm_Corpus_Callosum.nii.gz corndog_v3_wm_tr_cereb_rh_Cerebellar_Peduncle_Rostral.nii.gz corndog_v3_wm_tr_cereb_rh_Cerebellar_Peduncle_Caudal.nii.gz corndog_v3_wm_tr_cereb_lh_Cerebellar_Peduncle_Rostral.nii.gz corndog_v3_wm_tr_cereb_lh_Cerebellar_Peduncle_Caudal.nii.gz corndog_v3_wm_tr_cereb_Cerebellar_Peduncle_Middle.nii.gz corndog_v3_wm_tr_assoc_rh_UF.nii.gz - right uncinate fasciclulus corndog_v3_wm_tr_assoc_rh_SLF.nii.gz - right superior longitudinal fasciculus corndog_v3_wm_tr_assoc_rh_SFOF.nii.gz - right superior fronto-occipital fasciculus corndog_v3_wm_tr_assoc_rh_ILF.nii.gz - right inferior longitudinal fasciculus corndog_v3_wm_tr_assoc_rh_IFOF.nii.gz - right inferior fronto-occipital fasciculus corndog_v3_wm_tr_assoc_rh_Cingulum.nii.gz corndog_v3_wm_tr_assoc_lh_UF.nii.gz - left uncinate fasciclulus corndog_v3_wm_tr_assoc_lh_SLF.nii.gz - left superior longitudinal fasciculus corndog_v3_wm_tr_assoc_lh_SFOF.nii.gz - left superior fronto-occipital fasciculus corndog_v3_wm_tr_assoc_lh_ILF.nii.gz - left inferior longitudinal fasciculus corndog_v3_wm_tr_assoc_lh_IFOF.nii.gz - left inferior fronto-occipital fasciculus corndog_v3_wm_tr_assoc_lh_Cingulum.nii.gz corndog_v3_wm_tr_olfac_rh_OPT.nii.gz - right olfactory parietal tract corndog_v3_wm_tr_olfac_rh_OOT.nii.gz - right olfactory occipital tract corndog_v3_wm_tr_olfac_rh_OLT.nii.gz - right olfactory limbic tract corndog_v3_wm_tr_olfac_rh_OET.nii.gz - right olfactory entorhinal tract corndog_v3_wm_tr_olfac_rh_OCST.nii.gz - right olfactory corticospinal tract corndog_v3_wm_tr_olfac_lh_OPT.nii.gz - left olfactory parietal tract corndog_v3_wm_tr_olfac_lh_OOT.nii.gz - left olfactory occipital tract corndog_v3_wm_tr_olfac_lh_OLT.nii.gz - left olfactory limbic tract corndog_v3_wm_tr_olfac_lh_OET.nii.gz - left olfactory entorhinal tract corndog_v3_wm_tr_olfac_lh_OCST.nii.gz - left olfactory corticospinal tract Relationship between files, if important: These files include both the canine cortical atlas (Johnson et. Al 2020) and white matter subcortical atlas described in (TBD). This data set is also available at the NIH AFNI website https://afni.nimh.nih.gov/ METHODOLOGICAL INFORMATION Description of methods used for collection/generation of data: The data sets were generated from MRI data obtained from 30 mesaticephalic and dolichocephalic canines. This included 10 beagles and twenty mixed breed healthy dogs. Median age 5.5 years (IQR 7.5). MRI was performed invivo with all dogs undergoing anesthesia (Johnson et al 2020). MRI instrumentation included a 3.0T GU Discovery MR 750 scanning unit. 16 channel RF coil (Neo flex coil). T1W data protocol: 3D inversion recovery fast spoiled gradient echo BRAVO, isotropic voxels 0.5 mm3, TE = 3.6 ms, TR = 8.4 ms, TI = 450 ms, excitations = 3, flip angle 12, acquisition matrix size 256 x 256 DTI data protocol: TR=7000ms, TE=89.6ms, flip angle=90°, isotropic voxels 1.5mm3, 60 gradient directions, b=800 s/mm2 and a single unweighted (b=0) diffusion image Data processing to generate the population average template and cortical atlas are described in Johnson et. Al 2020. The white matter atlas was generated by manual delineation of white matter regions to divide the subcortical area into 61 regions. Additionally population average tractogram was created and dissected to provide masks of the major white matter pathways of the canine brain. Describe any quality-assurance procedures performed on the data: The resulting atlas and masks have been evaluated for anatomic accuracy. People involved with sample collection, processing, analysis and/or submission: Data collection: Philippa J. Johnson and Henning Voss Data Processing: Erica Andrews and Paul Taylor Atlas creation: Philippa J. Johnson and Fiona Inglis DATA-SPECIFIC INFORMATION FOR: These data can be viewed using software available at AFNI https://afni.nimh.nih.gov/ or using viewing systems such as FSLeyes https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes or ITKsnap http://www.itksnap.org/pmwiki/pmwiki.php