sepidhk / atlas-r2.0---stroke-lesion-segmentation

ATLAS R2.0 - Anatomical Tracings of Lesions After Stroke

ATLAS-R2.0---Stroke-Lesion-Segmentation

This is an example of the MR imaging is used to Segment Stroke-Lesion-Segmentation.

Prerequisities

The following dependencies are needed:

• numpy >= 1.11.1
• SimpleITK >=1.0.1
• pytorch-gpu ==1.10.0
• pandas >=0.20.1
• scikit-learn >= 0.17.1

How to Use

• 1、when download the all project,check out the data folder all csv,put your train data into same folder.or you can run ATLASR2.0data3dpreparewithSize.py to generate train data and validation data.
• 2、run ATLASR2.0_train.py for Unet3d segmeatation training:make sure train data have effective path
• 3、run ATLASR2.0_inference.py for Unet3d segmeatation inference:make sure test data have effective path

Result

• dice:train loss,train accuracy,validation loss,validation accuracy

• validation dataset segmentation result,left result is GT,right is predict

• more detail and trained model can follow my WeChat Public article.

Contact

• https://github.com/junqiangchen
• email: [email protected]
• Contact: junqiangChen
• WeChat Number: 1207173174
• WeChat Public number: 最新医学影像技术