Module bet 

Brain extraction.

• BET (run_bet): mesh-evolution Brain Extraction Tool. Smith, S.M. (2002). “Fast robust automated brain extraction.” Human Brain Mapping, 17(3):143-155. https://doi.org/10.1002/hbm.10062. Reference implementation: https://github.com/Bostrix/FSL-BET2
• HD-BET (hd_bet, onnx feature): nnU-Net deep-learning brain extraction; see hdbet.
• RS2-Net (rs2_net, onnx feature): deep-learning rodent brain extraction (mouse, rat); see rs2net.
• MindGrab (mindgrab, onnx feature): deep-learning brain extraction for any contrast; see mindgrab.

Re-exports

pub use hdbet::hd_bet;

pub use hdbet::hd_bet_memory_bytes;

pub use hdbet::hd_bet_network_input;

pub use hdbet::HdBetInference;

pub use hdbet::HdBetParams;

pub use rs2net::rs2_net;

pub use rs2net::Rs2NetParams;

pub use rs2net::RS2_NET_PATCH;

pub use mindgrab::mindgrab;

pub use mindgrab::MindGrabParams;

Modules

evolution 🔒

BET surface evolution algorithm

hdbet

HD-BET deep-learning brain extraction (onnx feature).

icosphere 🔒

Icosphere mesh generation

mesh 🔒

Mesh utilities for BET

mindgrab

MindGrab deep-learning brain extraction (onnx feature).

rs2net

RS2-Net rodent brain extraction (onnx feature).

Structs

BetParams

BET algorithm parameters

Enums

FslLeftRightOrder

How FSL stores an image’s left-right axis, which decides whether FSL flips it on reading (FslGetLeftRightOrder2, fslio.c; read_volume calls makeradiological()): an image whose sform (or, without one, qform) has a negative determinant is radiological and read as it is; one with a positive determinant is neurological and FSL reverses its x axis before bet2 sees it (and back when saving). The mesh is not symmetric, so the flip changes the mask.

Functions

run_bet

Run BET brain extraction, as FSL’s bet2 (see the module docs).