Hi, I would like to create a binary mask of the brain from dwi. I thought the following two steps should be ok:

1) 3dSkullstrip -input data.nii.gz -prefix data_skullstripped.nii.gz
2) 3dAutomask data_skullstripped.nii.gz -prefix data_masked.nii.gz

My questions:
1) Is there any reason I should perform 3dcalc afterward or should my mask be ready as is?
2) The output of 3dAutomask did not adhere to my prefix name. Instead, the output are .BRIK and .HEAD. Can I use the .BRIK file directly as my mask in 3dDWUncert?
3) Shouldn't the output of 3dSkullStrip be brain only? If you look at the attached file, it doesn't appear that way, which also seemed to screw up my mask. (note- this is only for some subjects. Others looked ok.)

Thank you very much for your input.