from niworkflows.utils.spaces import Reference, SpatialReferences
from smriprep.workflows.anatomical import init_anat_fit_wf

wf = init_anat_fit_wf(
   bids_root=".",
   output_dir=".",
   freesurfer=True,
   hires=True,
   longitudinal=False,
   msm_sulc=True,
   t1w=["sub-01/anat/sub-01_T1w.nii.gz"],
   t2w=["sub-01/anat/sub-01_T2w.nii.gz"],
   flair=["sub-01/anat/sub-01_acq-flair_T2w.nii.gz"],
   skull_strip_mode="force",
   skull_strip_template=Reference("MNI152NLin2009cAsym"),
   spaces=SpatialReferences([
      ("MNI152NLin6Asym", {}),
      ("T1w", {}),
   ]),
   skull_strip_fixed_seed=False,
   omp_nthreads=1,
   sloppy=False,
)