imageflowtech/ukbb-gnc-abdominal-segmentation

Abdominal Organ Segmentation of UK Biobank and GNC Studies

Abdominal Organ Segmentations of UK Biobank (UKBB) and German National Cohort (GNC) Studies

Getting Started

Abdominal organ segmentations for UKBB and GNC studies can be obtained with 4 straightforward steps below.

Obtaining Predictions

Arguments

Folder names can be set as preferred. Details of arguments that will be used in the script are as follows:

zip_folder        = Folder that contains downloaded zip files for each subject. 
nifti_folder      = Folder that contains subjects with stitched volumes as .nii.gz files
nnunet_folder     = Folder that contains subjects formatted for nnUNet
prediction_folder = Folder that contains final predictions
output_folder     = Folder that contains predictions with the original naming
dataset_name      = Either ukbb or gnc
num_channels      = Either 1 or 4

Step 0: Download data

Download and put whole-body MRI data into a single directory

Step 1: Run extract_ukbb.py or extract_gnc.py

This is the initial pre-processing step (only run either UKBB or GNC script depending on your source of data).

python extract_ukbb.py 
    --zip_folder my_original_data/ 
    --nifti_folder my_nifti_data/

Step 2: Run convert2nnunet.py

The script converts files to the nnUNet naming.

python convert2nnunet.py 
    --nifti_folder my_nifti_data/ 
    --nnunet_folder my_nnunet_data/ 
    --dataset_name ukbb 
    --num_channels 4

Step 3: Run predict.py

The script generates the predictions for abdominal organs (example below is for UKBB with 4-channel model).

CUDA_VISIBLE_DEVICES=0 
RESULTS_FOLDER=models/ 
python predict.py 
    --nnunet_folder my_nnunet_data/ 
    --prediction_folder my_predictions/ 
    --dataset_name ukbb 
    --num_channels 4

Step 4: Run convert2original.py

The script converts predictions back to the original naming.

python convert2original.py 
    --prediction_folder my_predictions/ 
    --output_folder my_outputs/

All organ segmentations are saved into the output folder with their original naming convention.