Brain T1w MRIs -> Remove artifacts in background


For my research project, I generate some brain MRIs (T1w) and I have a recurrent issue with some non-zero voxels generated in the background. Note that generated images are skull-stripped.
I would like to find a way or a tool for removing these artifacts. For example, I already tried with FSL-FAST, but all non-zero voxels are segmented as CSF even if they are clearly in the background. Maybe I there exists some FSL-FAST options which may help me but I don’t find them…

Thanks in advance for your help.


If you have a brain mask that is aligned with your T1, you can can intersect your T1 image with that mask with the fslmaths command. That should zero out any voxels outside the brain (unless your mask is also showing those weird out of brain voxels).


Thanks for your answer Steven,

I don’t have mask for generated images, in fact I would like to find a way to estimate a mask from the generated brain. I tested with FAST, but it segments artifacts outside brain as CSF.

You can try to use BET2 from FSL to extract the brain. If that doesn’t work, ANTs has more sophisticated tools.