In modern imaging diagnosis Magnetic Resonance Imaging (MRI) is possibly one of the widely used effective techniques particularly for brain tissue segmentation. Clustering techniques may not be perfect always. Clustering can be significantly improved by supervising partially. A novel partially supervised kernel induced rough fuzzy clustering is proposed for brain tissue segmentation by employing a small quantity of labeled pixels with constraint seeded policy. Labeled pixels act as the constraints which are utilized to initialize the clustering process and guide the method towards a more accurate partitioning. Kernel trick used here enhances the possibility of linear partition of different complex segments of brain which cannot separate linearly in its original feature space. Whereas, the rough and fuzzy set handles the overlappingness, vagueness and indiscernibility of different tissue regions. A variety of benchmark brain MRI datasets are used for the experiments. The ability of the method is compared with state-of-the-art clustering segmentation techniques and evaluated using different validity indices. Experimental results confirm that the technique considerably enhances the segmentation accuracy with a little quantity of supervision. Enhancement in accuracy gained by the method compared to the other techniques are 0.3, 0.37, 1.15, and 1.03% for IBSR datasets 144, 150, 155, and 167, respectively, and 1.02% for the BrainWeb dataset 85. Statistical impact of the method is confirmed from the paired t-test results.