This DATSETNAMEreadme.txt file was generated on 2019-09-21 by Philippa Johnson Edited 2019-09-05 to add dataset citation information (Wendy Kozlowski) ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Cortical Atlas of the Canine Brain 2. Author Information Principal Investigator Contact Information Name: Philippa Johnson Institution:Cornell University College of Veterinary Medicine Address: 930 Campus Road, Ithaca, NY 13081, USA Email: pjj43@cornell.edu or philippa.johnson@gmail.com Associate or Co-investigator Contact Information Name: Erica Barry Institution: Cornell University College of Veterinary Medicine Address: 930 Campus Road, Ithaca, NY 13081, USA Email: efb79@cornell.edu 3. Date of data collection: 2006-2009 4. Geographic location of data collection: Cornell Magnetic Resonance Imaging Facility, Martha Van Rensselaer Hall, Cornell University, Ithaca, NY. 5. Information about funding sources that supported the collection of the data: Funding provided by Cornell Feline Health Center -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: Data are shared under a CC0 declaration, but the authors request proper attribution. If you use this data, please cite it as: Johnson, Philippa J. and Erica F. Barry. (2019) 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 --------------------- DATA & FILE OVERVIEW --------------------- Note all files are zipped together using gzip, and individual in age files (.nii) are again zipped inside that. 1. File List A. Filename: Johnson_etal_2019_Canine_Atlas Short description: Canine population T1 template and cortical atlas for T1-weighted structural data with ROI keys and xml label file for structural T1 of 30 mesaticephalic/dolichocephalic canines. B. Foldername: TSMs Short description: Tissue segmentation masks (TSMs) for structural T1 of the canine population T1 template. C. Foldername: Lobe_masks Short description: Lobe masks and lobe label key text file for canine population atlas. D. Foldername: Hemispheres Short description: Cortical atlas for each hemisphere of the canine population atlas. 2. Relationship between files: Generated from the same cohort of 30 Canines. 3. Additional related data collected that was not included in the current data package: None 4. Are there multiple versions of the dataset? No -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Animals and Anesthesia This study was approved by Cornell University’s Institutional Animal Care and Use Committee. Thirty neurologically normal, mature (age at scanning mean = 6.4 years, standard deviation = 3.34 years), mixed sex (eight male and twenty-two female), canine were recruited from research populations. Dogs imaged for template creation were imaged under general anesthesia performed by a board-certified veterinary anesthesiologist. Dogs were premedicated with Dexmedetomidine (3mcg/kg Dexdomitor 0.5mg/ml, Zoetis Inc, Kalamazoo, MI), induced to general anesthesia with Propofol to effect (3.2-5.4mg/kg Sagent Pharmaceuticals, Schaumburg, III) and intubated. They were maintained under anesthesia with inhalant isoflurane and oxygen with a dexmedetomidine continuous rate infusion (1mcg/kg/hr Dexdomitor 0.5mg/ml, Zoetis Inc, Kalamazoo, MI). Anesthesia). Image Acquisition MRI was performed in a General Electric Discovery MR750 3-Tesla unit (60cm bore diameter), operating at 50mT/m amplitude and 200 T/m/s slew-rate. Subjects were placed in dorsal recumbancy with their head centered in a 16-channel medium flex radio-frequency coil (NeoCoil, LLC N27 W23910A Paul Rd. Pewaukee, WI 53072 USA © NeoCoil All rights reserved). A high resolution T1-weighted 3D inversion-recovery fast spoiled gradient echo sequence (Bravo) was performed in each subject with the following parameters; isotropic voxels 0.5mm3, TE=3.6ms, TR=8.4ms, TI=450ms, excitations =3, a flip angle of 12°, acquisition matrix size = 256 x 256 and slice thickness 0.5mm. 2. Methods for processing the data: T1 Image Preprocessing and Segmentation Isovolumetric T1-weighted data from the template group were used to create a population average atlas template. MRI data were corrected for low frequency inhomogeneity (Tustison et al., 2010). A manual removal of non-brain tissues was applied prior to registration and spatial normalization (Friston et al., 1995) The origin of images were manually set to the rostral commissure using SPM12 (Penny et al., 2007) and reoriented to a standard FMRI Software Library (FSL) orientation for inter-subject consistency (Jenkinson et al., 2012). Template Creation Previous atlas literature have tested linear and non-linear methods for template creation and consistently found non-linear registration using Advanced Normalization Tools (ANTs) to provide templates with the best contrast and signal to noise ratios (Nitzsche et al., 2018, 2015; Stolzberg et al., 2017). For this reason, we opted to use non-linear registration methods to create our population average template. The individual subjects T1s were averaged and transformed into a common space population template using Advanced Normalization Tools (ANTs) which applied affine registration and diffeomorphic registration via the symmetric normalization (SyN) algorithm using the ants multivariate template creation script (Avants et al., 2011, 2010 2008). This template was generated with a stereotaxic coordinate system according to the MNI template specifications and in line with other animal templates (Mandal et al., 2012; Nitzsche et al., 2018). The origin of the Cartesian system (x,y,z; 0,0,0) was centered on the mid-line over the dorsal aspect of the rostral commissure. The zero x-axis value sagittal plane extended through the center of the brain in line with the falx cerebri, the zero y axis value transverse plane was parallel to the anterior commissure and transected the brain symmetrically and the zero z axis value dorsal plane ran from the dorsal rostral commissure to the mesencephalic aqueduct, ventral to the caudal commissure. Sagittal plane x-axis values increased left to right, transverse plane y-axis values increased caudal to rostral and dorsal plane z-axis values increased ventral to dorsal. All co-ordinates are provided in millimeters. The final template was evaluated by a neuroanatomical expert and compared to anatomic specimens for appropriate anatomical detail. Tissue segmentation maps (TSMs) were created from the template using FMRIB’s Automated Segmentation Tool (FAST) which segments brain matter into cerebral spinal fluid, grey matter, and white matter while correcting for spatial intensity variations (Zhang et al., 2001). FAST was used to create partial volume maps, TPMs of each tissue type, binary segmentation masks and bias field maps. Binary segmentations were assessed anatomical coherence with the T1 weighted scan and manually corrected to control white matter overestimation from FAST. 3. People involved with sample collection, processing, analysis and/or submission: Philippa J. Johnson, Erica Barry, Wenming Luh, Ashish Raj, Sofia Cerda-Gonzalez ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [Johnson_etal_2019_Canine_Atlas] ---------------------------------------- 1. Number of files: 8 2. File List A. Name: Canine-labels.xml Description: xml file of ROI atlas parcellation labels, center of gravity for use with FSLEYES B. Name: Canine_population_template.nii Description: Average canine population T1 template C. Name: atlas_roi_key.txt Description: Text file of value and label for each ROI creating the whole brain atlas D. Name: whole_atlas_cortical.nii Description: Canine cortical brain atlas containing different values for each cortical ROI E. Name: whole_atlas_cortical_subcortical.nii Description: Canine cortical brain atlas containing different values for each cortical and subcortical ROI F. Name: Atlas_reference_table.csv Description: Table saved as a comma separated variable file, with the values, labels and description of each ROI in the canine population atlas. N/A represents areas that do not fall within a specific Gyri. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [Johnson_etal_2019_Canine_Atlas/Hemispheres] ----------------------------------------- 1. Number of files: 2 2. File List A. Name: left_hemisphere_cortical Description: Left hemisphere cortical atlas B. Name: right_hemisphere_cortical Description: Right hemisphere cortical atlas ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [Johnson_etal_2019_Canine_Atlas/Lobe_masks] ----------------------------------------- 1. Number of files: 9 2. File List A. Name: all_lobes.nii Description: File containing all lobe masks at different values B. Name: all_lobes_key.nii Description: File containing the values pertaining to each lobe for the all_lobe file C. Name: cingulate_lobe_mask.nii Description: Binary mask file for the cingulate lobe D. Name: frontal_lobe_mask.nii Description: Binary mask file for the frontal lobe E. Name: occipital_lobe_mask.nii Description: Binary mask file for the occipital lobe F. Name: parietal_lobe_mask.nii Description: Binary mask file for the parietal lobe G. Name: perisylvian_lobe_mask.nii Description: Binary mask file for the perisylvian (temporal) lobe H. Name: sensorymotor_lobe_mask.nii Description: Binary mask file for the sensory-motor lobe I. Name: subcortical_lobe_mask.nii Description: Binary mask file for the subcortical ROIs ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [Johnson_etal_2019_Canine_Atlas/TSMs] ----------------------------------------- 1. Number of files: 4 2. File List A. Name: Canine_population_template_TSM.nii Description: Tissue segmentation map (TSM) containing segmentations of cortical spinal fluid (csf), grey matter (gm) and white matter (wm) of the canine population T1 template B. Name: csf_mask.nii Description: Binary mask of cortical spinal fluid (csf) C. Name: gm_mask.nii Description: Binary mask of grey matter (gm) D. Name: wm_mask.nii Description: Binary mask of white matter (wm)