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more accidental linting
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psadil committed Oct 17, 2024
1 parent 166be74 commit ac5f87a
Showing 1 changed file with 7 additions and 13 deletions.
20 changes: 7 additions & 13 deletions sdcflows/workflows/fit/pepolar.py
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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()
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