Convert .mhd file to a 3D image that can be saved as a .ply

aotero54 · July 21, 2022, 9:27pm

Hello,

I have several mhd files that I am trying to convert into a 3D image that can be saved as a ply and thus have landmarks placed upon it. I am unsure of how to do this and other similar posts I have found have not been all to helpful while trying to do so on my own. Thank you for the help!

muratmaga · July 21, 2022, 9:48pm

MHD is a volumetric format, whereas PLYs are surface models. If you want to generate surface volumes from those MHD files, you will need to use the segmentation editor and segment the structures you would like to export to 3D model.
You may want to review this segmentation tutorial we created for SlicerMorph

github.com

SlicerMorph/Tutorials/blob/main/Segmentation/Segmentation.md

# Introduction to Image Segmentation with 3D Slicer
Segmentation is one of the most useful things you can do with Slicer! A segmentation is an abstract representation of structures in an image. It usually contains more than one segment (usually non-overlapping) annotated with different colors in 2D and 3D.

<p align="center">
<img src="images/turtle_seg.gif">
</p>

In Slicer, there two complementary modules that are used hand-in-hand for segmentation tasks.

1. `Segment Editor` is the module for creating segmentations of volumes. Segmentation (also known as contouring) delineate structures of interest. There are various manual and semiautomatic methods for generating your segmentations which we cover in the tutorial below.  
2. `Segmentations` is the module that allows you to control how the segmentations generated by `Segment Editor` are saved and exported. Some of the key functionality is to import/export segmentations into **LabelMap** or **3D Model** representations, adjust and edit display properties, copy/move segments across different segmentations, and so forth. 

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If you are new to image segmentation, it is a good ideas to read the [official **Image Segmentation** documentation from 3D Slicer.](https://slicer.readthedocs.io/en/latest/user_guide/image_segmentation.html) Even if you have previous experience with other 3D segmentation programs, it might be good to take a minute to read the Slicer specific functionalities and how different types of data types relate to each other (see figure below).

<img src="images/DataTypes.png">

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Convert .mhd file to a 3D image that can be saved as a .ply

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