Removal of the perfusion lag structure in the fMRI signal was combined with independent component analysis (ICA)-based cleaning to evaluate its effect on test-retest reproducibility. In HCP test-retest data from 40 subjects, either treatment and the combined method effectively improved the reproducibility of functional connectivity. However, the effect was more evident in between-subject similarity of the connectivity pattern than within-subject similarity. This finding suggests that the perfusion lag structure may be one of the sources of between-subject variability, that may degrade the functional connectivity.
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