shanpriya3

I am facing the same issue with 3D Unet for two class segmentation. Could someone help? Thanks!

Here is my configuration file: ############################ input configuration sections [ct] path_to_search = ./data/ct/ filename_contains = CT spatial_window_size = (96, 96, 96) pixdim = (1.0, 1.0, 1.0) interp_order = 3 axcodes=(A,...

Hello, Any update on this issue?

Hi, Thanks for your response. I did remove those 2 lines from my code. I have 3 classes/labels in total(including background) which have the values 0,1,2 in my ground-truth respectively....

Could you please explain what does these lines(189-192) do in train.py? tmp[tmp>=0.5] = 1 tmp[tmp0] = 1 tmp2[tmp2

Hi, I am getting the same error. Did you @fu123456 manage to solve this?

I don't get any results. The script stops working. I have downloaded, extracted copied the images and XML files in the corresponding folders Images folder: /LIDC-IDRI-Preprocessing/LIDC_Dataset/Images/LIDC-IDRI/LIDC-IDRI-0002…...LIDC-IDRI-1012/ LIDC-IDRI-xxxx has some folders...

I am using Ubuntu-18.04. Yes, I did path_to_executables="~/MITK-superbuild/MITK-build/bin" path_to_dicoms = "~/LIDC-IDRI-Preprocessing/LIDC_less/Img" path_to_xmls= "~/LIDC-IDRI-Preprocessing/LIDC_Dataset/XML_Data/LIDC-XML-only/tcia-lidc-xml/" path_to_nrrds = "~/LIDC-IDRI-Preprocessing/LIDC_Dataset/nrrd" path_to_planars= "~/LIDC-IDRI-Preprocessing/LIDC_Dataset/planars" path_to_characteristics=r"~/LIDC-IDRI-Preprocessing/LIDC_Dataset/characteristics.csv" path_to_error_file="~s/LIDC-IDRI-Preprocessing/LIDC_Dataset/conversion_error.txt" I tried using full path as well.

I am getting the above error

The path is pointing to the directory containing all patient folders, like "LIDC-IDRI-0205", "LIDC-IDRI-0206" etc... but