Voxel-Wise Tissue Segmentation and Partial Volume Quantification in Experimental EPI Space to Inform FMRI and FcMRI Analysis

Daniel L. Shefchik¹, Andrew S. Nencka¹, Andrzej Jesmanowicz¹, James S. Hyde¹

Tissue segmentation for functional MRI studies is normally performed with FreeSurfer, which utilizes T1 weighted anatomical images to provide tissue separation maps. The anatomical separation maps have a different image warping than EPI images and can lead to incorrect image registration. A different tissue separation method utilizes the GREASE-II sequence to produce T1, T2, and T2 relaxivity maps in the same EPI space as functional studies. The three EPI relaxivity maps produce CSF, gray and white matter maps by using their mean relaxivity values. Tissue maps are combined to view the Partial volume effect throughout the brains gray matter.