MRI skull stripping

Hello everyone
I am new to AFNI and in urgent need of skull stripping a large MRI dataset.
Would you mind helping me and giving me tips to find a way quickly?


Hi, Tannaz-

3dSkullStrip is the function for that.

The help therein has a few tips in it-- search for “Tips:” in the help file; you can view the helpfile most easily with:

3dSkullStrip -hview

probably (it should open the file up in a text editor in a separate window that you should be able to search through).


If you want to transform a T1-weighted dataset to MNI space and at the same time skull strip it, the @SSwarper script can do the job for you. It applies a combination of 3dSkullStrip and 3dQwarp to do these calculations.