suppl/0_renaming.md

Renaming files

The filenames of the images in the original datasets are complex or not unique. Thus, the following steps were performed:

TotalSegmentator

The TotalSegmentator images are all named ct.nii.gz, and must be renamed. To do so, you can run the following bash script within in the downloaded directory (e.g., Totalsegmentator_dataset_v201). Remove echo only after double checking.

for dir in */; do 
  echo mv -v "${dir}ct.nii.gz" "../tseg-${dir::-1}.nii.gz"
done

In this dataset, files derived from CT scans in the TotalSegmentator dataset are prefixed with tseg- followed by the corresponding TotalSegmentator ID (e.g., tseg-s1317.nii.gz).

VerSe

The VerSe images file names include descriptions of the scan, orientation and mask. To make the filenames more simple and uniform, we removed the unnecessary suffixes. To do so too, you can run the following bash commands within in the directory containing all downloaded NIfTI files. Remove echo only after double checking!

for f in *.nii.gz; do echo mv "$f" "${f/split-/}"; done
for f in *.nii.gz; do echo mv "$f" "${f/sub-/}"; done
for f in *.nii.gz; do echo mv "$f" "${f/_dir/}"; done
for f in *.nii.gz; do echo mv "$f" "${f/_ct/}"; done
for f in *.nii.gz; do echo mv "$f" "${f/-ax/}"; done
for f in *.nii.gz; do echo mv "$f" "${f/-iso/}"; done
for f in *.nii.gz; do echo mv "$f" "${f/-sag/}"; done

for file in *.nii.gz ; do
    echo mv -v "$file" "verse-${file}"
done

In this dataset, files derived from CT scans in the VerSe dataset are prefixed with verse- followed by the corresponding VerSe ID (e.g., verse-825.nii.gz).