White matter hyperintensity (WMH) has been considered the primary biomarker from small-vessel cerebrovascular disease to Alzheimer’s disease (AD) and has been reported for its correlation of brain structural changes. To perform WMH related analysis with brain structure, both T1-weighted (T1w) and (Fluid Attenuated Inversion Recovery(FLAIR) are required. However, in a clinical situation, it is limited to obtain 3D T1w and FLAIR images simultaneously. Also, the most of brain segmentation technique supports 3D T1w only. Therefore, we introduced the semi-supervised learning method that can perform brain segmentation using FLAIR image only. Our method achieved a dice overlap score of 0.86 for brain tissue segmentation on FLAIR, with the relative volume difference between T1w and FLAIR segmentation under 4.8%, which is just as reliable as the segmentation done by its paired T1w image. We believe our semi-supervised learning method has a great potential to be used to other MRI sequences and provide encouragement to people who seek brain tissue segmentation from a non-T1w image.