Scripts used to preprocess LIFE resting state data (based on J. Huntenburgs preprocessing scripts available on github (https://github.com/juhuntenburg/pipelines/tree/master/src/lsd_lemon))

Structural preprocessing (run_structural.py using structural.py) performs

• freesurfer segmentation if not yet done
• brain extraction based on freesurfer brain segmentation
• registration of the skull-stripped brain to MNI (2mm isotropic) space

Functional preprocessing (run_lemon_resting.py using lemon_resting.py) performs

• deletion of first 5 volumes
• coregistration of mean EPI to fieldmap magnitude scan and calculation of unwarping field
• motion correction
• applying unwarping and motion correction to time series
• slice time correction
• registration to 3mm isotropic MNI space
• smoothing
• visualizing and saving of .png images (functional and anatomical images overlaid)