Merge pull request #472 from eilidhmacnicol/fix/fast_bias_iters

FIX: set fast bias_iters parameter to 0

Author: mgxd

src/smriprep/interfaces/fsl.py

@@ -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

src/smriprep/workflows/anatomical.py

@@ -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
@@ -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,
         )