The results of this intermodal registration were examined visually for all 51 subjects in our data set using Freeview visualization tools, overlaying fMRI reference image, and delineated T1 scan. Figure 2B illustrates a sample result of our intermodal registration. As can be seen in the figure, FreeSurfer’s extracted region’s borders facilitate this visual inspection. This time-consuming process of visual inspection also examined the effect of EPI spatial distortion and B0 field inhomogeneity after intermodal registration. Even though this visual inspection did not reveal any major Inhibitors,research,lifescience,medical intermodal registration inaccuracy, it was a crucial step in our project as our data do not include

the reverse polarity acquisition which is often used for spatial distortion correction. Using the computed Inhibitors,research,lifescience,medical transformation matrix and FreeSurfer’s generated masks in the subject’s native space, the regional fMRI data were extracted from each subject’s data. At this stage, the extracted regional fMRI data are in each subject’s native space and stored separately for each subject and ROI. Only

one interpolation was used in the entire process of localization by combining the transformation parameters for all three realignments: (1) motion correction, (2) FreeSurfer to T1, and (3) T1 to averaged reference image in fMRI Inhibitors,research,lifescience,medical space. This minimizes the effect of nearest-neighbor interpolation Inhibitors,research,lifescience,medical errors in the final outcome. Ten regions of DMN were considered in this study and have been repeatedly reported in the literature (Andrews-Hanna et al. 2007; Buckner and Vincent 2007; Buckner et al. 2008; Raichle 2011). The names of the neuroanatomical regions in DMN and their abbreviations are as follows: hippocampus (Hi), entorhinal cortex (En), inferior parietal lobule (IP), isthmus of the cingulate (IC), medial orbitofrontal cortex Inhibitors,research,lifescience,medical (MOF), parahippocampal gyrus (PHi), posterior cingulate (PoC), precuneus

(PCu), superior-frontal gyrus (SF), and supramarginal gyrus (SM). Once the ten regional fMRI images were extracted separately for each subject, temporal BOLD signal was Carnitine palmitoyltransferase II calculated for each region by Ponatinib chemical structure averaging all voxels inside the region. For comparison purpose, we complemented the native space analysis with the prevailing spatial normalization and smoothing in SPM8 software package, whereas the rest of the processing pipeline remained the same. We used the MNI152 as the standard template and smoothing was done by a Gaussian kernel of full width at half maximum (FWHM) equal to 6 mm. The same DMN region masks in MNI152 template space were used to extract the 10 regional time series for every subject after spatial normalization and smoothing. To examine the effect of averaging the left and right hemispheres (Vincent et al. 2006; Andrews-Hanna et al. 2007; Buckner et al. 2008; Hedden et al.