Trouble obtaining data

[WillX1998]

Hi,

Does anyone know how to access the actual image data, not the segmentation images, without using Python? I'm trying to do my own segmentation using MATLAB.

Thank you.

[neheller]

I'm not very familiar with MATLAB. Are you able to run bash? This script should be able to download the imaging data. Make sure to run it from the repository root.

#!/bin/bash
if [ ! -d "data" ]
then
  mkdir data
fi
for I in {0..299}
do
  DSTP=$(printf "data/case_%05d" $I)
  DSTF=$(printf "data/case_%05d/imaging.nii.gz" $I)
  if [ ! -d $DSTP ]
  then
    mkdir $DSTP
  fi
  if [ ! -f $DSTF ]
  then
    wget https://kits19.sfo2.digitaloceanspaces.com/master_$(printf "%05d" $I).nii.gz
    mv master_$(printf "%05d" $I).nii.gz $DSTF
  fi
done

[WillX1998]

Hi,

Thank you for responding. I've never used Bash before. Is that the only way to download the imaging data?

[WillX1998]

Can you please walk me through using Git Bash to download the images? I tried running the code and it said the images were not found.

[neheller]

I'm not sure why the images wouldn't be found since it works on my end. There must be some other problem when using the above with Git Bash. How about the following MATLAB script?

if ~exist('data', 'dir')
    mkdir('data');
end
for i = 0:299
    case_dir = fullfile('data', sprintf('case_%05d', i));
    if ~exist(case_dir, 'dir')
        mkdir(case_dir);
    end
    websave(fullfile(case_dir, 'imaging.nii.gz'), sprintf('https://kits19.sfo2.digitaloceanspaces.com/master_%05d.nii.gz', i), 'timeout',20);
end

[WillX1998]

Hi I managed to get the images. Thank you!