Abstract
To develop a strategy for structural brain imaging when using FSL software for segmentation and subsequent volumetry. Three-dimensional (3D) structural MRI of 1-mm isotropic resolution was performed on a 3-Tesla clinical imaging system. Prescribed signal evolution of a multiple spin-echo (SE) sequence with variable refocusing flip angle for T2 weighting, and a modified driven equilibrium Fourier transform (MDEFT) sequence were used for T1 weighting. Postprocessing included rigid-body coregistration, brain extraction, and segmentation using the tools of the FSL 3.2 software package. T2 weighting provided reliable delineation of the subarachnoidal space, while T1 weighting provided better segmentation of gray matter (GM) and white matter (WM). The combination of T1-weighted (T1-w) and T2-w data allowed the identification of a T2-hypointense class of "nonbrain" (NB) representing larger vessels and structures of connective tissue, as well as partial volume of bone and air-filled cavities. Brain extraction on T2-w data and subsequent segmentation of the combined T1- and T2-w intensity distribution into four classes are recommended.
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