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Jason Kai edited this page Oct 1, 2021 · 2 revisions

Anatomical scans & brain masks

See BIDS standard

Transforms

Try to use ANTS whenever possible

bids(root=’work/<rule.smk_name>’,     
        datatype=’<dt>’,            
        subject=’{subject}’,                     
        from_=’<modality>’,        e.g. T1w
        to=‘<fixed_image>’,        e.g. MNI152NLin2009cAsym
        suffix=’<xfm_suffix>’      e.g. 0GenericAffine.mat, 1Warp.nii.gz, 1InverseWarp.nii.gz, Composite.h5, InverseComposite.h5
     )

Eg. bids(root=’work/preproc.smk’,datatype=’anat’,subject=’{subject}’,from_=’T1w’,to=config[‘template_MNI’],suffix=’1Warp.nii.gz’)