Hi Daniel,

Thanks for your reply. Ok, sounds good. I've attached an image with the raw epi overlay on the raw anat and you can see this bright signal is indeed CSF. For my analysis, I plan to extract the mean time series from a set of 90 ROIs registered in MNI space to form a functional connectivity matrix. Would you recommend that I mask out the CSF outside of the warped anatomical brain boundary using the mask_anat or mask_epi_anat image prior to extracting the time series?

Additionally, do you have any suggestions for the images where the brainstem is slightly off? I've attached an image here demonstrating the alignment issue with the brainstem/cerebellum. It seems in these instances that the other regions of the brain are relatively well aligned (e.g., ventricles, cortical gyri/sulci). Though I do have some regions of interest in the cerebellum where this might cause a slight issue. Would you suggest I attempt to adjust the alignment of these images to fix the brainstem issue or would you think this is ok to move forward?

Thanks,
Jenna