Fslmeants

# Extract a timecourse from fMRI (fmri_img) using a binary mask (mask_roi) 
# usually a standard space 4D fMRI dataset and some atlas-defined region.
# fslmeants extracts an average value for the roi at each time point
# and puts it in the txt file named after the -o flag.

fslmeants -i fmri_img -o fmri_img.txt mask_roi

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