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Fixed pre-commit #5

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merged 5 commits into from
Dec 11, 2024
Merged

Fixed pre-commit #5

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9f7ec30
Fixed pre-commit
spirosmaggioros Nov 22, 2024
9f78a42
Merge branch 'main' into spiros-dev
spirosmaggioros Nov 22, 2024
885eef9
Format utils.py and init.py
spirosmaggioros Nov 22, 2024
2a0c6af
Added build badges on readme
spirosmaggioros Nov 23, 2024
fa8f1c8
Correct torch version
spirosmaggioros Dec 11, 2024
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2 changes: 1 addition & 1 deletion DLWMLS/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -246,7 +246,7 @@ def main() -> None:
model_folder = os.path.join(
Path(__file__).parent,
"nnunet_results",
"Dataset004_Dataset003_qcedCorrected/nnUNetTrainer__nnUNetPlans__3d_fullres"
"Dataset004_Dataset003_qcedCorrected/nnUNetTrainer__nnUNetPlans__3d_fullres",
# "Dataset%s_Dataset%s_dlwmlsICVAll/nnUNetTrainer__nnUNetPlans__%s"
# "Dataset%s_Task%s_DLWMLSV2/nnUNetTrainer__nnUNetPlans__%s/"
# % (args.d, args.d, args.c),
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5 changes: 4 additions & 1 deletion DLWMLS/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,9 @@ def rename_and_copy_files(src_folder: str, des_folder: str) -> Tuple[dict, dict]
shutil.copy2(old_name, new_name)
rename_dict[filename] = rename_file
rename_back_dict[rename_back] = filename.split(".nii")[0] + "_WMLS.nii.gz"
print("%s will be renamed to %s" % (old_name, filename.split(".nii")[0] + "_WMLS.nii.gz"))
print(
"%s will be renamed to %s"
% (old_name, filename.split(".nii")[0] + "_WMLS.nii.gz")
)

return rename_dict, rename_back_dict
7 changes: 5 additions & 2 deletions README.md
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@@ -1,5 +1,8 @@
# DLWMLS - Deep Learning White Matter Lesion Segmentation

![MacOS Build](https://github.com/CBICA/DLWMLS/actions/workflows/macos-build.yml/badge.svg)
![Ubuntu Build](https://github.com/CBICA/DLWMLS/actions/workflows/ubuntu-build.yml/badge.svg)

## Overview

DLWMLS uses a trained [nnUNet](https://github.com/MIC-DKFZ/nnUNet) model to segment White Matter Lesions (WML) from ICV-segmented (see DLICV method) and LPS oriented brain images (Nifti/.nii.gz format).
Expand All @@ -17,7 +20,7 @@ pip install -e .
```

### Installing PyTorch
Depending on your system configuration and supported CUDA version, you may need to follow the [PyTorch Installation Instructions](https://pytorch.org/get-started/locally/).
Depending on your system configuration and supported CUDA version, you may need to follow the [PyTorch Installation Instructions](https://pytorch.org/get-started/locally/).

## Usage

Expand All @@ -34,7 +37,7 @@ DLWMLS -h
```

## \[Windows Users\] Troubleshooting model download failures
Our model download process creates several deep directory structures. If you are on Windows and your model download process fails, it may be due to Windows file path limitations.
Our model download process creates several deep directory structures. If you are on Windows and your model download process fails, it may be due to Windows file path limitations.

To enable long path support in Windows 10, version 1607, and later, the registry key `HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\FileSystem LongPathsEnabled (Type: REG_DWORD)` must exist and be set to 1.

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4 changes: 2 additions & 2 deletions requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
torch>=2.2.1
nnunetv2>=2.2.1
torch==2.2.1
nnunetv2==2.5.1
argparse
huggingface_hub
pathlib
4 changes: 2 additions & 2 deletions setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,9 +20,9 @@
download_url="https://github.com/CBICA/DLWMLS/",
url="https://github.com/CBICA/DLWMLS/",
packages=find_packages(exclude=["tests", ".github"]),
python_requires=">=3.8",
python_requires=">=3.9",
install_requires=[
"torch>=2.2.1",
"torch<=2.2.1",
"nnunetv2>=2.2.1",
"argparse",
"huggingface_hub",
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