Dear Paul,
Thank you for the reply. I actually just found the solution that I should be using fsl_regfilt rather than fsl_glm. When I use fsl_regfilt the resulting output correlates with the initial input at .86-.95, which is more along the lines of what I'd expect to be the correlations between the initial and the motion regressed data. I'm not sure why fsl_glm doesn't work. But fsl_regfilt does.
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