{"id":2338,"date":"2013-09-12T14:35:00","date_gmt":"2013-09-12T18:35:00","guid":{"rendered":"https:\/\/www.med.unc.edu\/psych\/research\/niral\/niral\/download\/software-pages\/makeatlasscripts-rodent\/"},"modified":"2018-09-24T15:00:13","modified_gmt":"2018-09-24T19:00:13","slug":"makeatlasscripts-rodent","status":"publish","type":"page","link":"https:\/\/www.med.unc.edu\/psych\/research\/niral\/download\/download-software\/makeatlasscripts-rodent\/","title":{"rendered":"MakeAtlasScripts-Rodent"},"content":{"rendered":"
\n

\"MakeAtlasScriptsLogo3\"<\/p>\n

Publication<\/h2>\n

For more information, read here<\/a><\/p>\n

Download<\/h2>\n\n\n\n\n
Platform<\/th>\nScripts<\/th>\nCMake<\/th>\nBatchMake 1.3<\/th>\nTools<\/th>\n<\/tr>\n
Linux<\/td>\nHere<\/a><\/td>\ncmake-2.8.11.2-Linux-i386.sh<\/a><\/td>\nIncluded in Tools<\/td>\n2014.10.09<\/span><\/p>\n

2015.05.14<\/span><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

To get the latest version of the script, download them from here<\/a>.<\/p>\n

Download an external brain atlas<\/h2>\n

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<\/a>)<\/p>\n\n\n\n\n\n\n\n
Atlas<\/th>\n<\/tr>\n
Mouse 3D MR minimum deformation atlas<\/td>\n<\/tr>\n
Waxholm Space atlas of the mouse brain<\/a><\/td>\n<\/tr>\n
Rat P72 (also contains probability maps). Segmentations also available here<\/a><\/td>\n<\/tr>\n
Mouse – C57BL6 Brookhaven atlas (also contains probability maps)<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

To generate your own probability maps, please refer to the following papers:<\/p>\n