Is there any open source software that can be used to segment image data (dicom) and the segmented data can be exported as volume or mesh data for further FE analysis?
Dear Muhammad
I suggest you to use one o software from below list. they are so useful for your purpose:
I hope that it would be helpful.
Regards
Dear Ali,
Thank you very much for your detailed answer.
I do not just want to visualize the dicom images but want to segment various organs and then export the volumes as mesh/volume data for further FE analysis. I know Simpleware and Materialize Mimics software are capable of doing that but these are not free. However, I'll check if any of your suggestions can serve my purpose.
Many many thanks for your help.
Dear Muhammad
thanks.
I used specially "ezDICOM" and "3D Doctor" (a limited free version) in my research. they can be useful to export volume data.
Regards
Hi Muhammad,
We use 3D Slicer (http://slicer.org/), which is a very versatile medical imaging platform. It loads your DICOM, you can segment it manually, semi-automatically, or even automatically for some organs, and then export the segmentation to volume or surface mesh. The community is very helpful, as are the wiki pages.
Hi Csaba,
Thank you very much for your guidance. I have tried 3D slicer. Image segmentation and visualization is very easy and convenient with 3D slicer. It can export the segmented volume in .stl format. But I failed to export the segmentation as volume. However, I'll go through the tutorials to learn the export details. Thanks again for your helpful suggestions.
Thanks for the update! If you segmented with Editor, or a module that yields a volume, then you can use the Save data button, and choose some volume format, like NRRD or MHA. If it's a model, then you can convert it to a volume using the Model to LabelMap module, or the Contours mechanism in the SlicerRT extension.
The tool ITK-SNAP is exclusively developed for [medical] image segmentation tasks. Available here:
http://www.itksnap.org/pmwiki/pmwiki.php
Just to keep things up-to-date: The new Segment Editor tool in 3D Slicer is a completely overhauled manual and semi-automated segmentation module, and is competitive in terms of ease-of use with ITK snap and superior in features
http://slicer.readthedocs.io/en/latest/user_guide/module_segmenteditor.html
We are developing MedSeg - a free online segmentation tool for CT and MRI with AI capabilities that you can take a look at: http://medseg.ai
Not open source, but it is free to use and no installation is needed. Otherwise, if you have the time to learn how to use a more advanced tool, then I would suggest like many others 3D Slicer. It has loads of great functions, but is not the most user friendly for radiologists if all you need is to create a segmentation.
Another good open source option is RIL-contour: https://gitlab.com/Philbrick/rilcontour
Sir, there is a nice open-source platform for medical image processing (.dcm, .dicom) with Python. This Python library's name is MedPy. I found if very familiar for image segmentation.
link: https://pypi.org/project/MedPy/
All documentations are available there.
The main downside is : it needs some python coding. No GUI.
please check out these links:
https://www.postdicom.com/en/blog/medical-imaging-software
http://www.wohlersassociates.com/medical2018.pdf
MedSeg (free, web-based): http://medseg.ai
regards
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