diff --git a/sdcflows/workflows/fit/pepolar.py b/sdcflows/workflows/fit/pepolar.py index ef892e33d8..928a2b5e5b 100644 --- a/sdcflows/workflows/fit/pepolar.py +++ b/sdcflows/workflows/fit/pepolar.py @@ -141,23 +141,19 @@ def init_topup_wf( SortPEBlips(), name="sort_pe_blips", run_without_submitting=True ) # Merge into one 4D file - concat_blips = pe.Node( - MergeSeries(affine_tolerance=1e-4), name="concat_blips" - ) + concat_blips = pe.Node(MergeSeries(affine_tolerance=1e-4), name="concat_blips") # Pad dimensions so that they meet TOPUP's expectations pad_blip_slices = pe.Node(PadSlices(), name="pad_blip_slices") # Run 3dVolReg between runs: uses RobustAverage for consistency and to generate # debugging artifacts (typically, one wants to look at the average across uncorrected runs) - setwise_avg = pe.Node( - RobustAverage(num_threads=omp_nthreads), name="setwise_avg" - ) + setwise_avg = pe.Node(RobustAverage(num_threads=omp_nthreads), name="setwise_avg") # The core of the implementation # Feed the input images in LAS orientation, so FSL does not run funky reorientations - to_las = pe.Node( - ReorientImageAndMetadata(target_orientation="LAS"), name="to_las" - ) + to_las = pe.Node(ReorientImageAndMetadata(target_orientation="LAS"), name="to_las") topup = pe.Node( - TOPUP(config=str(data.load(f"flirtsch/b02b0{'_quick' * sloppy}.cnf"))), + TOPUP( + config=str(data.load(f"flirtsch/b02b0{'_quick' * sloppy}.cnf")) + ), name="topup", ) # "Generalize" topup coefficients and store them in a spatially-correct NIfTI file @@ -166,9 +162,7 @@ def init_topup_wf( ) # Average the output - ref_average = pe.Node( - RobustAverage(num_threads=omp_nthreads), name="ref_average" - ) + ref_average = pe.Node(RobustAverage(num_threads=omp_nthreads), name="ref_average") # Sophisticated brain extraction of fMRIPrep brainextraction_wf = init_brainextraction_wf()