COVID-19 SEGMENTATION

USE FOR EXTRACTIN COVID MASKS FROM VTI CT_IMAGES

1- It is necessary to extract the lung and slice the image , using the pipeline can be done the following way:

Let`s say that we want to slice case 174 and the vti file is named CASE174.vti The file that will do the required task is named prepare_vti.py and the command to call it is the following:

python3 prepare_vti.py -i {path_to/CASE174.vti} -m {path_to/CASE174_mask.vti} -d1 {path_to/CASE174} -d2 {path_to/CASE59_MASK} -n {path_to/SEGMENTED_SLICES} -e {path_to/segmented_lung174.vti}

• -i path to vti image
• -m path to and the name you want to save the 3d mask
• -d1 dir where you want to save original image slices
• -d2 dir where you want to save mask slices
• -n dir where you want to save segmented slices
• -e dir where you want to save segmented lung before slicing it

2- Run the COV-19 Segmentation network with the following command

python3 main.py -m {test} -model {path_to/segnet_norm.pth} -d1 {path_to/SEGMENTED_SLICES} -d2 {path_to/CASE174_PRED/} -n {covid_mask_case174.vti} -i {path_to/CASE174.vti} -f {device} -md {path_to/Sliced_Mask}

• -m running mode, in this case should always be test, it changes only if u want to train
• -model path to the model weights
• -d1 path to segmented slices obtained from step 1
• -d2 path to dir where you want to save the network prediction and the assambled vti file
• -n name of the assambled vti
• -i path to the original vti
• -f runnning device, cpu or gpu

Extract Trachea

python3 trachea_segmentation.py -p {path to original vti} -t {path where to save the trachea segmented vti}

Extract Trachea

Extract Lung and Trachea on the same vti

python3 full_lungSegmentation.py -p {path to original vti} -t {path where to save the trachea segmented vti} -l {path where to save lung mask}