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" teeth
If you leave the task name off, AutoSeg prompts for it during runtime:
autoseg "C:\path\to\scans"
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.
1 maintainer
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file autoseg-1.0.2.tar.gz.
File metadata
- Download URL: autoseg-1.0.2.tar.gz
- Upload date:
- Size: 3.9 kB
- Tags: Source
- Uploaded using Trusted Publishing? Yes
- Uploaded via:
twine/7.0.0 CPython/3.13.14
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
af9419635698cb408f781343617ae703c73cb0b573656530855728a83f4df2c1
|
|
| MD5 |
b8b42f85e29c680fb6c8a9456893d208
|
|
| BLAKE2b-256 |
d47501981acbe07059038a4555b87ab6a89d612e3dfa878d7273cc74ca7af3e3
|
Provenance
The following attestation bundles were made for autoseg-1.0.2.tar.gz:
Publisher:
publish.yml on Z-ttack/AutoSeg
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
autoseg-1.0.2.tar.gz -
Subject digest:
af9419635698cb408f781343617ae703c73cb0b573656530855728a83f4df2c1 - Sigstore transparency entry: 2349192629
- Sigstore integration time:
-
Permalink:
Z-ttack/AutoSeg@84c3de86c89b7aad94e5866dce1bede423b30cf9 -
Branch / Tag:
refs/tags/v1.0.2 - Owner: https://github.com/Z-ttack
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
publish.yml@84c3de86c89b7aad94e5866dce1bede423b30cf9 -
Trigger Event:
release
-
Statement type:
File details
Details for the file autoseg-1.0.2-py3-none-any.whl.
File metadata
- Download URL: autoseg-1.0.2-py3-none-any.whl
- Upload date:
- Size: 4.4 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? Yes
- Uploaded via:
twine/7.0.0 CPython/3.13.14
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
aca20dd52c4ad5bdb5e614427b8a6d68f3d55dcd9e95d918dfec2e120922343c
|
|
| MD5 |
ad1b8cf661534ce50441dfe20e8f31b2
|
|
| BLAKE2b-256 |
d7e630c4952a9a0d3733d90af3528c8d1fc059feb23afc0ed4d8c17f0122be7b
|
Provenance
The following attestation bundles were made for autoseg-1.0.2-py3-none-any.whl:
Publisher:
publish.yml on Z-ttack/AutoSeg
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
autoseg-1.0.2-py3-none-any.whl -
Subject digest:
aca20dd52c4ad5bdb5e614427b8a6d68f3d55dcd9e95d918dfec2e120922343c - Sigstore transparency entry: 2349193303
- Sigstore integration time:
-
Permalink:
Z-ttack/AutoSeg@84c3de86c89b7aad94e5866dce1bede423b30cf9 -
Branch / Tag:
refs/tags/v1.0.2 - Owner: https://github.com/Z-ttack
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
publish.yml@84c3de86c89b7aad94e5866dce1bede423b30cf9 -
Trigger Event:
release
-
Statement type:
