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bugSomething isn't workingSomething isn't working
Description
Description
When rotating an image in the registration the edges require padding. When including skull stripping by specifying a bet path in the modalities everything works smoothly. However, when only performing registration, the padding values seem to be the mean across the image causing "grey boxes". Passing ants.apply_transform's parameter "defaultvalue" does not change the outcome.
Versions
antspyx==0.6.1
brainles_preprocessing==0.6.3
Reproducability
To reproduce place "t1c.nii.gz" and "flair.nii.gz" in the same directory as this script and run it:
from pathlib import Path
from brainles_preprocessing.modality import Modality, CenterModality
from brainles_preprocessing.normalization.percentile_normalizer import (
PercentileNormalizer,
)
from brainles_preprocessing.preprocessor import AtlasCentricPreprocessor
from brainles_preprocessing.registration import ANTsRegistrator
def main_no_skullstrip():
patient_folder = Path(".")
percentile_normalizer = PercentileNormalizer(
lower_percentile=0.1,
upper_percentile=99.9,
lower_limit=0,
upper_limit=1,
)
center = CenterModality(
modality_name="t1c",
input_path=patient_folder / "t1c.nii.gz",
normalizer=percentile_normalizer,
normalized_skull_output_path="no_skull_strip/t1c_normalized.nii.gz"
)
moving_modalities = [
Modality(
modality_name="flair",
input_path=patient_folder / "flair.nii.gz",
normalizer=percentile_normalizer,
normalized_skull_output_path="no_skull_strip/flair_normalized.nii.gz",
)
]
# Adding this registrator yields the same result as using the default one
registrator = ANTsRegistrator(transformation_params={"defaultvalue": 0})
preprocessor = AtlasCentricPreprocessor(
center_modality=center,
moving_modalities=moving_modalities,
registrator=registrator,
)
preprocessor.run()
if __name__ == "__main__":
main_no_skullstrip()Metadata
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bugSomething isn't workingSomething isn't working