This paper proposed a self-initialization process to K-Means method for automatic segmentation of human brain Magnetic Resonance Image (MRI) scans. K-Means clustering method is an iterative approach and the initialization process is usually done either manually or randomly. In this work, a method has been proposed to make use of the histogram of the gray scale MRI brain images to automatically initialize the K-means clustering algorithm. This is done by taking the number of main peaks as well as their values as number of clusters and their initial centroids respectively. This makes the algorithm faster by reducing the number of iterations in segmenting the MRI image. The proposed method is named as Histogram Based Self Initializing K-Means (HBSIKM) method. Experiments were done with the MRI brain volumes available from Internet Brain Segmentation Repository (IBSR). Similarity validation was done by Dice coefficient with the available gold standards from the IBSR website. The performance of the proposed method is compared with the traditional K-Means method. For the IBSR volumes, the proposed method yields 3 to 4 times faster results and higher dice value than traditional K-Means method.