When viewing brainmask.mgz in Freeview, for some subjects the brain is slightly (~10-20 degrees) rotated. By looking at the raw data, I see that their head position in the scanner was slightly skewed. 

I thought  that brainmask.mgz is created after Talairach transformation and normalization has been completed. I took this to mean that the brainmask.mgz file has been registered to an atlas. If so, shouldn't the brainmask.mgz files for all subjects appear with 0 rotation in freeview? Should I be concerned that this is not the case for my dataset?

Thanks for your help!

Reema

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