Hi Mark,
I performed the FLIRT command that you suggested and lo and behold my ROI mask in now wonderfully oriented to MNI space and I no longer get an error when I'm running it in FEAT! Thanks so much!
I had one last question though. When I look at it in FSLView, the intensity of the mask ranges from 1-70 from voxel to voxel. Do I need to remake the mask so that the intensity is always 1? Someone told me this had to be done for pre-threshold masking.
Cheers,
Dave
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