Merge pull request #158 from jhlegarreta/FixNilearnNiftiWarning

ENH: Copy NIfTI image header when creating from image

Author: effigies

nireports/assembler/report.py

@@ -285,7 +285,7 @@ def __init__(
         }
         meta_repl.update({kk: vv for kk, vv in metadata.items() if isinstance(vv, str)})
         meta_repl.update(bids_filters)
-        expr = re.compile(f'{{({"|".join(meta_repl.keys())})}}')
+        expr = re.compile(f"{{({'|'.join(meta_repl.keys())})}}")
 
         for line in bootstrap_file.read_text().splitlines(keepends=False):
             if expr.search(line):

nireports/reportlets/modality/dwi.py

@@ -80,7 +80,7 @@ def plot_dwi(dataobj, affine, gradient=None, **kwargs):
             if gradient is None
             else f"""\
 $b$={gradient[3].astype(int)}, \
-$\\vec{{b}}$ = ({', '.join(str(v) for v in gradient[:3])})"""
+$\\vec{{b}}$ = ({", ".join(str(v) for v in gradient[:3])})"""
         ),
         **kwargs,
     )

nireports/reportlets/mosaic.py

@@ -35,12 +35,14 @@
 import matplotlib as mpl
 import matplotlib.pyplot as plt
 import nibabel as nb
+import nilearn
 import numpy as np
 import numpy.typing as npt
 from matplotlib.gridspec import GridSpec
 from nibabel.spatialimages import SpatialImage
 from nilearn import image as nlimage
 from nilearn.plotting import plot_anat
+from packaging.version import Version
 from svgutils.transform import SVGFigure, fromstring
 
 from nireports.reportlets.utils import (
@@ -89,7 +91,10 @@ def plot_segs(
     )
 
     if masked:
-        bbox_nii: SpatialImage = nlimage.threshold_img(bbox_nii, 1e-3)  # type: ignore[no-redef]
+        if Version(nilearn.__version__) >= Version("0.11"):
+            bbox_nii: SpatialImage = nlimage.threshold_img(bbox_nii, 1e-3, copy_header=True)  # type: ignore[no-redef]
+        else:
+            bbox_nii: SpatialImage = nlimage.threshold_img(bbox_nii, 1e-3)  # type: ignore[no-redef]
 
     cuts = cuts_from_bbox(bbox_nii, cuts=7)
     out_files = []