Merge pull request #7 from CBICA/localdownload

Pull changes from localdownload

DLICV/src/.gitattributes

@@ -0,0 +1,35 @@
+*.7z filter=lfs diff=lfs merge=lfs -text
+*.arrow filter=lfs diff=lfs merge=lfs -text
+*.bin filter=lfs diff=lfs merge=lfs -text
+*.bz2 filter=lfs diff=lfs merge=lfs -text
+*.ckpt filter=lfs diff=lfs merge=lfs -text
+*.ftz filter=lfs diff=lfs merge=lfs -text
+*.gz filter=lfs diff=lfs merge=lfs -text
+*.h5 filter=lfs diff=lfs merge=lfs -text
+*.joblib filter=lfs diff=lfs merge=lfs -text
+*.lfs.* filter=lfs diff=lfs merge=lfs -text
+*.mlmodel filter=lfs diff=lfs merge=lfs -text
+*.model filter=lfs diff=lfs merge=lfs -text
+*.msgpack filter=lfs diff=lfs merge=lfs -text
+*.npy filter=lfs diff=lfs merge=lfs -text
+*.npz filter=lfs diff=lfs merge=lfs -text
+*.onnx filter=lfs diff=lfs merge=lfs -text
+*.ot filter=lfs diff=lfs merge=lfs -text
+*.parquet filter=lfs diff=lfs merge=lfs -text
+*.pb filter=lfs diff=lfs merge=lfs -text
+*.pickle filter=lfs diff=lfs merge=lfs -text
+*.pkl filter=lfs diff=lfs merge=lfs -text
+*.pt filter=lfs diff=lfs merge=lfs -text
+*.pth filter=lfs diff=lfs merge=lfs -text
+*.rar filter=lfs diff=lfs merge=lfs -text
+*.safetensors filter=lfs diff=lfs merge=lfs -text
+saved_model/**/* filter=lfs diff=lfs merge=lfs -text
+*.tar.* filter=lfs diff=lfs merge=lfs -text
+*.tar filter=lfs diff=lfs merge=lfs -text
+*.tflite filter=lfs diff=lfs merge=lfs -text
+*.tgz filter=lfs diff=lfs merge=lfs -text
+*.wasm filter=lfs diff=lfs merge=lfs -text
+*.xz filter=lfs diff=lfs merge=lfs -text
+*.zip filter=lfs diff=lfs merge=lfs -text
+*.zst filter=lfs diff=lfs merge=lfs -text
+*tfevents* filter=lfs diff=lfs merge=lfs -text

README.md

@@ -1,42 +1,36 @@
-### DLICV - Deep Learning Intra Cranial Volume
+# DLICV - Deep Learning Intra Cranial Volume
 
 ## Overview
 
 DLICV uses a trained [nnUNet](https://github.com/MIC-DKFZ/nnUNet) model to compute the intracranial volume from structural MRI scans in the nifti image format, oriented in _**LPS**_ orientation.
 
 ## Installation
 
-# As a python package
+### As a python package
 ```bash
 pip install DLICV
 ```
-# Directly from this repository
+### Directly from this repository
 ```bash
 git clone https://github.com/CBICA/DLICV
 cd DLICV
 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/). 
+
 ## Usage
-A pre-trained nnUNet model can be found at our [hugging face account](https://huggingface.co/nichart/DLICV) or at [DLICV-V2 v1.0.0 release](https://github.com/CBICA/DLMUSE/releases/tag/v1.0.0).
+A pre-trained nnUNet model can be found at our [hugging face account](https://huggingface.co/nichart/DLICV).
 Feel free to use it under the package's [licence](LICENCE)
 ```bash
-DLICV -i "input_folder" -o "output_folder" -device cuda/cpu/mps
+DLICV -i "input_folder" -o "output_folder" -device cpu
 ```
 
-You can perform one example test run using the test input folder by running
-```bash
-DLICV -i test_input/DLICV_test_images -o test_input/DLICV_test_results -device cuda
-```
 
 ## Contact
 For more information, please contact [CBICA Software](mailto:[email protected]).
 
 ## For developers
 Contributions are welcome! Please refer to our [CONTRIBUTING.md](CONTRIBUTING.md) for more information on how to report bugs, suggest enhancements, and contribute code.
-If you're a developer looking to contribute, you'll first need to set up a development environment. After cloning the repository, you can install the development dependencies with:
-
-```bash
-pip install -r requirements.txt
-```
-This will install the packages required for running tests and formatting code. Please make sure to write tests for new code and run them before submitting a pull request.
+Please make sure to write tests for new code and run them before submitting a pull request.

requirements.txt

@@ -1,4 +1,4 @@
-torch==2.2.1
+torch>=2.2.1
 nnunetv2==2.5.1
 argparse
-huggingface_hub
+huggingface_hub

setup.py

@@ -13,21 +13,21 @@
 
 setup(
     name="DLICV",
-    version="1.0.0",
+    version="1.0.1",
     description="DLICV - Deep Learning Intra Cranial Volume.",
     long_description=long_description,
     long_description_content_type="text/markdown",
-    author="Ashish Singh, Guray Erus, Vishnu Bashyam, George Aidinis",
+    author="Ashish Singh, Guray Erus, Vishnu Bashyam, George Aidinis, Alexander Getka",
     author_email="[email protected]",
-    maintainer="George Aidinis, Spiros Maggioros, Kyunglok Baik",
-    maintainer_email="[email protected], [email protected], [email protected]",
+    maintainer="George Aidinis, Spiros Maggioros, Kyunglok Baik, Alexander Getka",
+    maintainer_email="[email protected], [email protected], [email protected], [email protected]",
     download_url="https://github.com/CBICA/DLICV/",
     url="https://github.com/CBICA/DLICV/",
     packages=find_packages(exclude=["tests", ".github"]),
     python_requires=">=3.8",
     install_requires=required,
     entry_points={
-        "console_scripts": ["DLICV = src.__main__:main"]
+        "console_scripts": ["DLICV = DLICV.__main__:main"]
         },
     classifiers=[
                     "Intended Audience :: Developers",