I’m attempting to use freesurfer’s
BBRegister to coregister a structural image to the functional images of a subject.
So far I did
RECON = Node(ReconAll(directive="all"), name="RECON") RECON.inputs.subjects_dir = "/freesurfer" bbreg = Node(BBRegister(init="fsl", contrast_type="t2"), name="bbreg")
when connecting the nodes what file should I specify as the source_file of bbregister, should it be the brainmask from reconall output?
wf.connect(RECON, bbreg, [("brainmask","source_file")])
Also, how can I specify the reference image (the image that doesn’t move) in
BBRegister in order to align the anatomical image with the realigned EPIs?