AutoSeg

AutoSeg runs TotalSegmentator on every .nii or .nii.gz file inside a folder tree.

Given a root folder, it searches that folder and all subfolders for NIfTI files, runs:

TotalSegmentator -i <input_file> -o <output_folder> -ta <task>

and saves each segmentation output beside the source scan.

Requirements

• Python 3.9 or newer
• TotalSegmentator installed and available on your command line

Install TotalSegmentator separately before using this package. You should be able to run:

TotalSegmentator --help

Install

After this package is published to PyPI, users will be able to install it with:

pip install autoseg

Task Argument

AutoSeg adds the -ta flag to the TotalSegmentator command for you. You only need to provide the task name:

autoseg "C:\path\to\scans" total

Usage

Run AutoSeg on a folder:

autoseg "C:\path\to\scans" total

Use another TotalSegmentator task by passing the task name after the folder:

autoseg "C:\path\to\scans" <task name>

If you leave the task name off, AutoSeg prompts for it during runtime:

autoseg "C:\path\to\scans"

Use TotalSegmentator's --statistics option for volume and intensity calculations

autoseg "C:\path\to\scans" <task name> statistics

Preview what would run without starting TotalSegmentator (Reduced wait time for testing/troubleshooting):

autoseg "C:\path\to\scans" total --dry-run

Output Folders

For each input file, AutoSeg creates a segmentation folder in the same directory as the scan.

Example:

C:\data\patient01\scan.nii.gz
C:\data\patient01\scan_segmentations\

If the expected output folder already exists and contains files, AutoSeg skips that scan so it does not run segmentation again.

AutoSeg also ignores folders named segmentations or ending in _segmentations. This prevents a resumed run from trying to segment TotalSegmentator's own output .nii.gz mask files.