Hi Freesurfer Experts,

I am trying to apply a mask that I made with FSL's bet to a NIFTI file that I got from someone else.

The mask looks fine, the NIFTI file is in float format, does not contain NaNs or negative values, but the overall values are all pretty low (in the 40ies). When I try to apply the mask to the NIFTI file using mri_mask, the output I get is essentially a copy of the mask (only zeros and ones). The same happens if I use fslmaths.

Any advice would be very much appreciated.

Thanks, Caspar

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