Download the Pig Brain Atlas

These downloads contain the three-dimensional MRI-based averaged brain and atlas of the young domesticated pig (Sus scrofa domestica) and accompanying material.

File details

Pig atlas versions

• 2.1 (released 7/21/2023): Updated 4-week-old and 12-week-old atlases, each with 30 regions of interest and 4 tissue probability maps. Discrepancies across the various thresholds, combined maps, and tissue probability maps in V.2.0 were addressed.
• 2.0 (released 4/1/2021): Updated 4-week-old pig brain atlas and 12-week old pig brain atlas, each with 26 regions of interest and 4 tissue probability maps identified. Read the article
• 1.2 (updated 12/12/2016): Includes updated tissue segmentations nifti (.nii) files. Read the article
• 1.1: Original atlas file (no longer available)

FILE CONTENTS

Version 2.1

The following changes were made to the version 2.0 files as follows:

• Pig Brain Atlases
  • A threshold of 200 was applied to the V.2.0 4-week-old atlas to remove excess matter that was not part of the brain.
  • A threshold of 600 was applied to the V.2.0 12-week-old atlas to remove excess matter that was not part of the brain.
  • The 12-week-old atlas was cropped and centered.
• Regions of Interest (ROI)
  • This folder now contains binary image files of 30 regions of interest. The following new regions were added:
    • Nucleus Accumbens
    • Putamen
    • Substantia Nigra
    • Third Ventricle
  • Discrepancies (i.e., inconsistent values across thresholds and orientation issues) across the three different thresholds, 0% [ROI_thr0], 25% [ROI_thr25], and 50% [ROI_thr50] were addressed in both 4-week-old and 12-week-old atlases.
  • All 12-week-old ROIs were cropped and centered.
• ROI Combined Maps 
  • Discrepancies (i.e., inconsistent labeling and orientation issues) across the threshold maps were addressed in the 4-week-old and 12-week-old maps.
  • A new priority list for labels was created. ROI labels were changed for both 4-week-old and 12-week-old atlases.
  • A maximum likelihood approach was utilized to create these maps meaning that certain regions of lower priority and lower threshold are not displayed or only have a few voxels in the combined maps. A full breakdown comparing the number of voxels and volume of each separate ROI binary map and combined threshold map is provided in the included Excel workbook:
    • Pig_MRI_Atlas_V2.1_ROI_and_Combined_Voxel_Volume_Comparison
• Tissue Probability Maps
  • Inconsistency in threshold labeling for Not_Brain_Map was addressed in both 4-week-old and 12-week-old atlases. Not_Brain_Map is now fully binary.
• Pig_FA_Standard
  • A fractional anisotropy template is now available for both 4-week-old and 12-week-old pigs.

Version 2.0

The download file contains the following files in the ".gz" format:

• Pig Brain Atlas – This is the averaged brain image file.
• Regions of Interest – This folder contains binary image files of twenty-six regions of interest provided at three different thresholds, 0% [ROI_thr0], 25% [ROI_thr25], and 50% [ROI_thr50]. Additionally, files labeling the entire left side and right side of the atlas are provided.
• ROI Combined – This folder contains images that have all of the regions of interest (at the different thresholds) compiled. The label number for each region of interest can be found in the accompanying “ROI_Labels.xlsx” file.
• Tissue Probability Maps – This folder contains the gray matter, white matter, cerebrospinal fluid, and NotBrain tissue probability maps.
• Pig_FA_Standard – This is a standard fractional anisotropy template to be used for Tract-Based Spatial Statistics (TBSS).This file is only available for the 4-week-old pig.

Version 1.2

The download file contains the following files in the ".gz" format:

• Piglet_Averaged_Brain.nii - This is the averaged brain image file.
• ROI_Combined.nii - This is the image file that has all of the regions of interest compiled. The label number for each region of interest can be found in the accompanying "ROI_Labels.xlsx" file.
• ROI_Labels folder - This folder contains binary image files of each region of interest.
• Raw_Tissue_Segmentation folder - This folder contains the raw tissue probability maps for grey, white, and CSF tissues
• Smoothed_Tissue_Segmentation folder - This folder contains the tissue probability maps that have been smoothed with a full-width at half maximum (FWHM) of 1x1x1 mm.

LICENSE

Illinois Open Source License
Copyright © 2013, The Board of Trustees of the University of Illinois. All rights reserved.

Developed by:
The Pig Imaging Group
University of Illinois, Urbana Champaign
http://pigmri.illinois.edu

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal with the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimers. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimers in the documentation and/or other materials provided with the distribution.
Neither the names of , nor the names of its contributors may be used to endorse or promote products derived from this Software without specific prior written permission.

THE SOFTWARE IS PROVIDED "AS IS";, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.