repo contains scripts used to download and view the `Pediatric-CT-SEG` dataset

Jordan, P., Adamson, P. M., Bhattbhatt, V., Beriwal, S., Shen, S., Radermecker, O., Bose, S., Strain, L. S., Offe, M., Fraley, D., Principi, S., Ye, D. H., Wang, A. S., Van Heteren, J., Vo, N.-J., & Schmidt, T. G. (2021). Pediatric Chest/Abdomen/Pelvic CT Exams with Expert Organ Contours (Pediatric-CT-SEG) (Version 2) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.X0H0-1706

https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=89096588

bash download-tcia-file.sh

for example with code here: https://github.com/pangyuteng/tcia-image-download-python

export inputdir=/mnt/hd2/data/ped-ct-seg
python download.py Pediatric-CT-SEG-Mar-22-2022-manifest.tcia $inputdir

docker build -t pediatric-ct-seg .


docker tag pediatric-ct-seg pangyuteng:pediatric-ct-seg
docker push pangyuteng:pediatric-ct-seg

docker run -it -u $(id -u):$(id -g) -w $PWD -v /mnt:/mnt pediatric-ct-seg bash

mkdir -p /mnt/hd2/data/ped-ct-seg-nifti

python dcm2nifti.py \
    /mnt/hd2/data/ped-ct-seg \
    /mnt/hd2/data/ped-ct-seg-nifti