As I intend to get the additional skull and scalp surfaces created by betsurf.
In the UserGuide, it states that Bet2 has mutually exclusive option of
A This runs both bet2 and betsurf programs in order to get the additional skull and scalp surfaces created by betsurf. This involves registering to standard space in order to allow betsurf` to find the standard space masks it needs.
-S This attempts to cleanup residual eye and optic nerve voxels which bet2 can sometimes leave behind. This can be useful when running SIENA or SIENAX, for example. Various stages involving standard-space masking, morphpological operations and thresholdings are combined to produce a result which can often give better results than just running bet2.
--B This attempts to reduce image bias, and residual neck voxels. This can be useful when running SIENA or SIENAX, for example. Various stages involving FAST segmentation-based bias field removal and standard-space masking are combined to produce a result which can often give better results than just running bet2.
As I intend to cleanup residual eye and optic nerve voxels, and residual neck voxel before creating the additional skull and scalp surface,
If the input is a t1 weighted image is t1.nii.gz, what should the step of step procedure be?
Thanks.
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