This involves registering to standard space in order to allow betsurf` to find the standard space masks it needs. A This runs both bet2 and betsurf programs in order to get the additional skull and scalp surfaces created by betsurf. Because it is normally important (in this application) that masking be liberal (ie that there be little risk of cutting out valid brain voxels) the -f threshold is reduced to 0.3, and also the brain mask is "dilated" slightly before being used. This is principally intended for use on FMRI data, for example to remove eyeballs. F This option uses bet2 to determine a brain mask on the basis of the first volume in a 4D data set, and applies this to the whole data set. This is achieved by padding the end slices in both directions, copying the end slices several times, running bet2 and then removing the added slices. Z This can improve the brain extraction if only a few slices are present in the data (i.e., a small field of view in the Z direction). 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. This can be useful when running SIENA or SIENAX, for example. B This attempts to reduce image bias, and residual neck voxels. 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. S This attempts to cleanup residual eye and optic nerve voxels which bet2 can sometimes leave behind. The iterations stop when the centre-of-gravity stops moving, up to a maximum of 10 iterations. By iterating in this way the centre-of-gravity should move up each time towards the true centre, resulting in a better final estimate. The primary purpose is to improve the brain extraction when the input data contains a lot of non-brain matter - most likely when there is a lot of neck included in the input image. R This option runs more "robust" brain centre estimation it repeatedly calls bet2, each time using the same input image and the same main options, except that the -c option (which sets the starting centre of the brain estimation) is set each time to the centre-of-gravity of the previously estimated brain extraction. Variations on default bet2 functionality (mutually exclusive options): t apply thresholding to segmented brain image and mask c centre-of-gravity (voxels not mm) of initial mesh surface. r head radius (mm not voxels) initial surface sphere is set to half of this g vertical gradient in fractional intensity threshold (-1->1) default=0 positive values give larger brain outline at bottom, smaller at top f fractional intensity threshold (0->1) default=0.5 smaller values give larger brain outline estimates
n don't generate the default brain image output s generate rough skull image (not as clean as what betsurf generates)
o generate brain surface outline overlaid onto original image However, it also allows various additional behaviour. betsmallz has been replaced by the -Z option in bet.īy default bet just calls the bet2 program for simple brain extraction. betpremask has been replaced by the -b option in standard_space_roi. betfunc has been replaced by the -F option in bet. betall has been replaced by the -A and -A2 options in the new bet script.