Calling what was mapped here a 'connectome' is REALLY stretching it. When they make those graphs of parcels connected to each other, what they're doing is just measuring the correlation between activity as revealed by an fMRI (which is itself removed from activity, measuring the short-term fluctuations in bloodflow as a result of energy requirements) in different parcels of brain and drawing a 'connection' when the coefficient is high enough. Correlation is not just connection.
I do note that there was diffusion tensor imaging (which shows you the average orientation of fibers in any given voxel [and showed an unusual crossing mixed fiber feature in a spot of his corpus callosum and will probably show similar oddities throughout the brain in any given human] ) and I will try to get at that information once I am past a paywall later on, but the repeated MRIs appear to be fMRIs.
I don't think the paper is paywalled: link
MRIs: a lot of different scans including 15 T1 and T2 weighted structural scans; 19 diffusion-weighted scans. fMRI was mostly resting state (100), but also included various tasks such as n-back (15x), motion discrimination/stop signal (8x), object localiser (8x), verbal working memory localiser (5x), spatial WM (4x), breath holding (18x).
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