diff --git a/.DS_Store b/.DS_Store index fd67311..9a84326 100644 Binary files a/.DS_Store and b/.DS_Store differ diff --git a/DLWMLS/__main__.py b/DLWMLS/__main__.py index 0431c60..e8a2603 100644 --- a/DLWMLS/__main__.py +++ b/DLWMLS/__main__.py @@ -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), diff --git a/DLWMLS/utils.py b/DLWMLS/utils.py index cb3bad8..7fc5262 100644 --- a/DLWMLS/utils.py +++ b/DLWMLS/utils.py @@ -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 diff --git a/README.md b/README.md index 5420b3d..09ef3c2 100644 --- a/README.md +++ b/README.md @@ -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). @@ -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 @@ -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. diff --git a/requirements.txt b/requirements.txt index c1496e0..b53f4e7 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ -torch>=2.2.1 -nnunetv2>=2.2.1 +torch==2.2.1 +nnunetv2==2.5.1 argparse huggingface_hub pathlib diff --git a/setup.py b/setup.py index 384973f..25c52bc 100644 --- a/setup.py +++ b/setup.py @@ -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",