Dear Yan,

Thank you for your interest in the Waxholm Space atlas of the Sprague Dawley rat brain.

Do I understand correctly that you need NIfTI files containing one atlas region per file, i.e. separate files for individual regions?

If so, the fastest way to get there would be to use Convert3D, the command-line companion to ITK-SnAP:
http://www.itksnap.org/pmwiki/pmwiki.php?n=Convert3D.Convert3D (download from SourceForge)

Here is how to extract one region (represented by one label):
https://sourceforge.net/p/c3d/git/ci/master/tree/doc/c3d.md#-retain-labels-retain-labels-in-a-label-image

For example, to create a volume containing label 25 only:

Best regards,
Eszter