ENH: Increase threshold for PET brain mask

Author: mnoergaard

fmriprep/workflows/pet/confounds.py

@@ -579,6 +579,28 @@ def _binary_union(mask1, mask2):
     return str(out_name)
 
 
+def _smooth_binarize(in_file, fwhm=10.0, thresh=0.2):
+    """Smooth ``in_file`` with a Gaussian kernel and binarize at ``thresh``."""
+    from pathlib import Path
+
+    import nibabel as nb
+    import numpy as np
+    from scipy.ndimage import gaussian_filter
+
+    img = nb.load(in_file)
+    data = img.get_fdata(dtype=np.float32)
+    zooms = np.array(img.header.get_zooms()[:3], dtype=float)
+    sigma = (fwhm / 2.3548) / zooms
+    smoothed = gaussian_filter(data, sigma=sigma)
+    mask = smoothed > (thresh * smoothed.max())
+
+    out_img = img.__class__(mask.astype('uint8'), img.affine, img.header)
+    out_img.set_data_dtype('uint8')
+    out_name = Path('smoothed_bin_mask.nii.gz').absolute()
+    out_img.to_filename(out_name)
+    return str(out_name)
+
+
 def _carpet_parcellation(segmentation, crown_mask, nifti=False):
     """Generate a segmentation for carpet plot visualization."""
     from pathlib import Path

fmriprep/workflows/pet/fit.py

@@ -357,15 +357,18 @@ def init_pet_fit_wf(
 
     # Stage 4: Estimate PET brain mask
     from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms
-    from niworkflows.interfaces.nibabel import Binarize
 
-    from .confounds import _binary_union
+    from .confounds import _binary_union, _smooth_binarize
 
     t1w_mask_tfm = pe.Node(
         ApplyTransforms(interpolation='MultiLabel', invert_transform_flags=[True]),
         name='t1w_mask_tfm',
     )
-    petref_mask = pe.Node(Binarize(thresh_low=0.2), name='petref_mask')
+    petref_mask = pe.Node(
+        niu.Function(function=_smooth_binarize), name='petref_mask'
+    )
+    petref_mask.inputs.fwhm = 10.0
+    petref_mask.inputs.thresh = 0.2
     merge_mask = pe.Node(niu.Function(function=_binary_union), name='merge_mask')
 
     if not petref2anat_xform:
@@ -380,7 +383,7 @@ def init_pet_fit_wf(
             (inputnode, t1w_mask_tfm, [('t1w_mask', 'input_image')]),
             (petref_buffer, t1w_mask_tfm, [('petref', 'reference_image')]),
             (petref_buffer, petref_mask, [('petref', 'in_file')]),
-            (petref_mask, merge_mask, [('out_mask', 'mask1')]),
+            (petref_mask, merge_mask, [('out', 'mask1')]),
             (t1w_mask_tfm, merge_mask, [('output_image', 'mask2')]),
             (merge_mask, outputnode, [('out', 'pet_mask')]),
         ]