# FullAuto_VolumeStraightened_3dS 

## About this work

This pack allows to obtain a volume straightened, using a DICOM dataset and points of reference.

For this development was used 3DSlicer (v.5.2.1 built 2022-11-24), and the extensions SlicerVMTK (v.1.4.0) and Sandbox (v.8235ee8). On the other hand, the libraries in python needed are os, pil, pynrrd and numpy, and they must be installed in 3dS.

## How to use

**Tout d'abord**: Verify version and correct installation of the required extensions, version of 3dSlicer, libraries, and inputs formats.

Then, only two steps need to be followed:

1) Take the file *FullAutoStraight_alone.py* from the folder *FullAutoStraight_alone*, copy this file in the folder of 3dSlicer, then open it and check the directions of the folders of volumes, points and outputs.
2) From the terminal in the folder of 3dS, write in Linux or Win:
    - ./Slicer --python-script "FullAutoStraight_alone.py" --no-splash --no-main-window
    - Slicer.exe --python-script "FullAutoStraight_alone.py" --no-splash --no-main-window

**Extra**: if the points are not provided, then the extension GetPointsModule (same name folder) can be installed, then the user can select the points manually using the GUI of 3dS, and save them like a json file ready for use.

## Important sites

Some recomended sites in relation of 3dS are:

- [ ] [Oficial site](https://www.slicer.org/)
- [ ] [Community](https://discourse.slicer.org/)
- [ ] [ReadTheDocs](https://slicer.readthedocs.io/en/latest/)

## Disclaimer

This work is under active development; methods, extensions, soft and versions can change.

[Contact](mailto:lstel@idiap.ch).
[Diversion](http://www.koalastothemax.com/).