1.) Please refer to the NiIStat notes: the polarity of NiiStat is reverse of VLSM/NPM. Rather, NiiStat follows the standard statistical convention that a positive association means that a brighter image correlates with higher behavioral scores. We tend to draw lesions as bright voxels (1) on a black (0) background. The reason for the change is that NiiStat is designed for many modalities (CBF, MD, FA) and therefore keeping the standard statistical mode makes sense
 https://www.nitrc.org/plugins/mwiki/index.php/niistat:MainPage#Notes