When I load aal.nii.gz (from MRICRON) as a “Volume mask or atlas (MNI space)”, the Creating scouts showed having loaded 116 regions, however the number of loaded regions was less than 116? Why and how to solve this problem?
The AAL atlas is a volume atlas, while your source model is a surface.
The menu you use tries to guess which of your surface vertices belong to which volume region. Some AAL regions are not corresponding to any vertex on the cortex surface, therefore you would have less than 116 surface scouts created.
Btw, we added recently extra entries in the dialog window to load an atlas to create only non-overlapping regions:
Volumetric ROI Overlap Using Standard Volume Atlases
Note that the accuracy of this procedure is low. It is recommended to use surface-based atlases for surface source models and volume atlases with volume source models.
Thanks a lot.