Dear Mike,
> I have an average gray matter mask (binarized) [...] some regions/voxels of my mask are regarded as gray matter
That sounds reasonable, doesn't it. ;-) So I guess your mask includes voxels which are not GM, and you want to remove them. Just in case, maybe your files are alright anyway. Due to different normalization algorithms MNI space output is not necessarily identical to another MNI image. And of course it's going to depend on the particular threshold, e.g. maybe the template was created based on a stricter GM probability threshold.
SPM12 includes a ROI tool (load an image, right-click & chose "ROI tool" / Launch, then you can access additional options via right-click & "ROI tool"), although it might be rather confusing in your case. I'd suggest to go with MRIcroN as you already seem to work with that program, drawing ROIs is quite straightforward and there are also options to save the ROI as a binary image (which you could then use to mask the original image within SPM via Imcalc), but also to save masked versions of the raw image.
Best
Helmut
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