Accurate segmentation of different brain tissue types is an important step in the study of neuronal activities using functional magnetic resonance imaging (fMRI). Traditionally, due to the low spatial resolution of fMRI data and the absence of an automated segmentation approach, human experts often resort to superimposing fMRI data on high resolution structural MRI images for analysis. The recent advent of fMRI with higher spatial resolutions offers a new possibility of differentiating brain tissues by their spatio-temporal characteristics, without relying on the structural MRI images. In this paper, we propose a patch-wise deep learning method for segmenting human brain tissues into five types, which are gray matter, white matter, blood vessel, non-brain and cerebrospinal fluid. The proposed method achieves a classification rate of 84.04% and a Dice similarity coefficient of 76.99%, which exceed those by several other methods.