You need to be very careful that the coordinate system you use matches the atlases you use. For example, SPM normalizes brains to have an average size, whereas the MNI template is larger than average. This is shown in Figure 1 of Horn et al. (2017)
  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6050588/
I would suggest you consider using Lead-DBS which integrates Surfice
  https://www.lead-dbs.org
MRIcroGL and Surfice will work with any coordinate system, but you need to be careful to choose the same coordinate system for all stages of your processing and visualization.