3dSkullStrip on phase images using a mask


I am new to using AFNI and have a question regarding using the skull strip feature. I have successfully used 3dSkullStrip to remove the skull of my anatomical imaging, but I also phase images from a susceptibility weighted sequence. I tried performing the skull stripping on the phase imaged directly, but the results were poor. I noticed that there is a way to produce a mask using 3dSkullStrip, so I wanted to create the mask from my anatomical image and apply it to my phase image. However, I do not know how to apply the mask once I have it. Is there a separate function that would allow me to do this?

Thank you.

you can apply 3dcalc to mask the phase image, for example as follows

3dcalc -a phase.nii -b mask.nii -expr ‘a*b’ -prefix phase_masked.nii

Hope this helps,