Since previous functional connectivity studies [4] (link) with diffuse optical tomography showed similar maps using either HbO2, or HbR contrast, here we used only ΔHbO2 data for the connectivity analyses. Data were filtered to the functional connectivity band (0.009–0.08 Hz) following previous human functional connectivity algorithms [35] (link). While one might expect the frequencies involved in functional connectivity to scale with the size of the animal (as does heart and respiratory rate), studies of fcMRI in rat have used the same frequencies as found in humans [13] (link), [16] (link), [64] (link). Our results also demonstrate that low frequency fluctuations in mice predominately exist below 0.1 Hz. A representative power spectrum for a pixel's time trace before and after processing is shown in Fig. S9 . After filtering, each pixel's time series was resampled from 30 Hz to 1 Hz for further analysis. The time traces of all pixels defined as brain were averaged to create a global brain signal. This global signal was regressed from every pixel's time trace to remove global sources of variance.
Using the atlas as a reference, seed locations were chosen at coordinates expected to correspond to the left and right visual, motor, somatosensory, frontal, cingulate, and retrosplenial cortices as well as the right and left superior colliculi and olfactory bulbs. A 0.5 mm diameter circle at each seed location was averaged to create a seed time trace. These seed traces were correlated against every other brain pixel to create functional connectivity maps. Because seed-based methods are dependent on the seed location, we also used seed-independent methods for determining connectivity patterns. The time traces in every pixel were correlated against every other pixel to create an N×N connectivity matrix (where N is the number of pixels defined as brain). This matrix contains all the functional connectivity information that could be gained from seed-based analysis, but has too much data to examine all at once. Taking the SVD of this matrix will yield an ordered set of orthogonal singular vectors that represent the spatial connectivity patterns. The associated singular values indicate the extent to which a particular singular vector contributes to the total variance in the data. The first few singular vectors thus demonstrate the most dominant connectivity patterns.
Using the atlas as a reference, seed locations were chosen at coordinates expected to correspond to the left and right visual, motor, somatosensory, frontal, cingulate, and retrosplenial cortices as well as the right and left superior colliculi and olfactory bulbs. A 0.5 mm diameter circle at each seed location was averaged to create a seed time trace. These seed traces were correlated against every other brain pixel to create functional connectivity maps. Because seed-based methods are dependent on the seed location, we also used seed-independent methods for determining connectivity patterns. The time traces in every pixel were correlated against every other pixel to create an N×N connectivity matrix (where N is the number of pixels defined as brain). This matrix contains all the functional connectivity information that could be gained from seed-based analysis, but has too much data to examine all at once. Taking the SVD of this matrix will yield an ordered set of orthogonal singular vectors that represent the spatial connectivity patterns. The associated singular values indicate the extent to which a particular singular vector contributes to the total variance in the data. The first few singular vectors thus demonstrate the most dominant connectivity patterns.
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