The preprocessed fMRI volume data were then transformed onto the six laminar surface reconstructions using the transformation matrix obtained in the previous step above. An average time series was extracted from the whole thalamus. This was done, because our first hypothesis involved the M-type thalamus cells distributed in each nucleus of thalamus [59–64]. Next, time series from each vertex in 34 lateral cortical ROIs in the DK atlas [9] were extracted, separately for left and right hemispheres in each subject. The 68 ROIs’ mean time series corresponding to the cortical ROIs were extracted for each of the 6 layers (Fig. 2). The regions in the DK atlas are defined on an inflated surface by manually tracing from the depth of one sulcus to another, thus incorporating the gyrus within. Therefore, unlike volume based ROIs that are affected by the folding pattern of sulci and gyri, the surface-based definition of DK atlas ROIs means that the results are not affected by the gyral and sulcal folding patterns.
