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  • $\begingroup$ The first figure above refers to an experiment with the same visual stimulus presented every time. There is a different figure and movie for those data. The second figure above refers to a different experiment in which the stimuli are visual stimuli with differing orientations, the traces in the 2nd figure above are colored to simply correspond to differing visual stimuli orientations. $\endgroup$ Commented Nov 26, 2014 at 15:26
  • $\begingroup$ Also, you are correct that the original vector $\mathbf Y$ is chopped up to lengths of $\hat {\mathbf T}$ $\n$ $\endgroup$ Commented Nov 26, 2014 at 15:34
  • $\begingroup$ You have confused me by discussing $\mathbf V$ and $\mathbf S$ in the equation $$\mathbf J = \mathbf U^\top \mathbf Y.$$ Do you mean the first 2 or 3 columns of $\mathbf U$? $\endgroup$ Commented Nov 26, 2014 at 15:50
  • $\begingroup$ I've re-arranged things. Apologies, was a left over from before I sorted something else out. $\endgroup$ Commented Nov 26, 2014 at 16:07
  • $\begingroup$ Thanks for all your help. Is the first principal component weights vector just the mean time series collapsing across all voxels? If it were the mean, it would result in the smallest scores to fit to the individual data traces. $\endgroup$ Commented Nov 26, 2014 at 19:09