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FIX: set fast bias_iters parameter to 0 #472

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Merged
merged 8 commits into from
Apr 30, 2025
Merged

FIX: set fast bias_iters parameter to 0 #472

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60c60b6
fix: add fast interface allowing bias_iters=0
eilidhmacnicol Apr 30, 2025
67074c6
fix: drop in patched fast interface
eilidhmacnicol Apr 30, 2025
a33118a
fix: set bias_iters=0
eilidhmacnicol Apr 30, 2025
1f6132d
sty: ruff [skip ci]
eilidhmacnicol Apr 30, 2025
b24f945
Apply suggestions from code review
eilidhmacnicol Apr 30, 2025
3ae1804
tst: add test for fast interface
eilidhmacnicol Apr 30, 2025
75a8d24
sty: ruff
eilidhmacnicol Apr 30, 2025
401cc22
fix: fast doctest
eilidhmacnicol Apr 30, 2025
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28 changes: 28 additions & 0 deletions src/smriprep/interfaces/fsl.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,28 @@
from nipype.interfaces.base import traits
from nipype.interfaces.fsl.preprocess import FAST as _FAST
from nipype.interfaces.fsl.preprocess import FASTInputSpec


class _FixTraitFASTInputSpec(FASTInputSpec):
bias_iters = traits.Range(
low=0,
high=10,
argstr='-I %d',
desc='number of main-loop iterations during bias-field removal',
)


class FAST(_FAST):
"""
A replacement for nipype.interfaces.fsl.preprocess.FAST that allows
`bias_iters=0` to disable bias field correction entirely

>>> from smriprep.interfaces.fsl import FAST
>>> fast = FAST()
>>> fast.inputs.in_files = 'sub-01_desc-warped_T1w.nii.gz'
>>> fast.inputs.bias_iters = 0
>>> fast.cmdline
'fast -I 0 -S 1 sub-01_desc-warped_T1w.nii.gz'
"""

input_spec = _FixTraitFASTInputSpec
5 changes: 3 additions & 2 deletions src/smriprep/workflows/anatomical.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,7 @@
import smriprep

from ..interfaces import DerivativesDataSink
from ..interfaces.fsl import FAST
from ..utils.misc import apply_lut as _apply_bids_lut
from ..utils.misc import fs_isRunning as _fs_isRunning
from .fit.registration import init_register_template_wf
Expand Down Expand Up @@ -947,14 +948,14 @@ def init_anat_fit_wf(
# Stage 3: Segmentation
if not (have_dseg and have_tpms):
LOGGER.info('ANAT Stage 3: Preparing segmentation workflow')
fsl_ver = fsl.FAST().version or '(version unknown)'
fsl_ver = FAST().version or '(version unknown)'
desc += f"""\
Brain tissue segmentation of cerebrospinal fluid (CSF),
white-matter (WM) and gray-matter (GM) was performed on
the brain-extracted T1w using `fast` [FSL {fsl_ver}, RRID:SCR_002823, @fsl_fast].
"""
fast = pe.Node(
fsl.FAST(segments=True, no_bias=True, probability_maps=True),
FAST(segments=True, no_bias=True, probability_maps=True, bias_iters=0),
name='fast',
mem_gb=3,
)
Expand Down
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