MakeAtlasScripts-Rodent

Publication

For more information, read here

Download

Platform	Scripts	CMake	BatchMake 1.3	Tools
Linux	Here	cmake-2.8.11.2-Linux-i386.sh	Included in Tools	2014.10.09 2015.05.14

To get the latest version of the script, download them from here.

Download an external brain atlas

Download one of the atlas below, or any other atlas containing at least one “grayscale” image, one parcellation image, and probability maps. If no probability map is available, you create those images by thresholding the “grayscale” image (see reference)

Atlas
Mouse 3D MR minimum deformation atlas
Waxholm Space atlas of the mouse brain
Rat P72 (also contains probability maps). Segmentations also available here
Mouse – C57BL6 Brookhaven atlas (also contains probability maps)

To generate your own probability maps, please refer to the following papers:

• Evaluation of Atlas based Mouse Brain Segmentation, Lee et al., Proc SPIE. 2009 February 1; 7259: 725943–725949.

• Automatic Skull-stripping of Rat MRI/DTI Scans and Atlas Building, Oguz et al, Proc Soc Photo Opt Instrum Eng. 2011 March; 7962: 796225-1–796225-7.

Installation of a Midas server (this part is not necessary and the development of the scripts for the Midas server has been discontinued)

Find more information and download here

Documentation

Download the pdf here