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Merged
merged 3 commits into from
Jul 23, 2024
Merged

Update preprocessing_tutorial.ipynb #50

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2779dde
Update preprocessing_tutorial.ipynb
evamariie Apr 28, 2024
7c6fcfe
Update preprocessing_tutorial.ipynb
evamariie Apr 28, 2024
c97d024
Third try at black formatting
evamariie Apr 28, 2024
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10 changes: 8 additions & 2 deletions preprocessing/preprocessing_tutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -228,7 +228,13 @@
"from brainles_preprocessing.brain_extraction import HDBetExtractor\n",
"from brainles_preprocessing.modality import Modality\n",
"from brainles_preprocessing.preprocessor import Preprocessor\n",
"from brainles_preprocessing.registration import NiftyRegRegistrator\n",
"from brainles_preprocessing.registration import (\n",
" ANTsRegistrator,\n",
" NiftyRegRegistrator,\n",
" eRegRegistrator,\n",
")\n",
"\n",
"# ANTSRegistrator (default), NiftyRegRegistrator (Linux), eRegRegistrator (experimental)\n",
"\n",
"\n",
"def preprocess_exam_in_brats_style(inputDir: str) -> None:\n",
Expand Down Expand Up @@ -319,7 +325,7 @@
" preprocessor = Preprocessor(\n",
" center_modality=center,\n",
" moving_modalities=moving_modalities,\n",
" registrator=NiftyRegRegistrator(),\n",
" registrator=ANTsRegistrator(),\n",
" brain_extractor=HDBetExtractor(),\n",
" # optional: we provide a temporary directory as a sandbox for the preprocessin\n",
" temp_folder=\"temporary_directory\",\n",
Expand Down