Also, looking in the forum, I just found out that FSLview seems to save the mask files ONLY in .hdr because IT'S A BUG of Ubuntu!
In order to save them in .nii you need to open FSL or FSLview from the terminal.
Here more infos --> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;10b2ef5c.1203
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