Import OsiriX ROI as segmentation

Hello,
I have ima files and their segmentation data as xml / rois_seris file formats. How can I import segmentations to 3D Slicer and create 3D models out of them? Are these file formats supported in the segmentation module?
Thanks,

I’m not familiar with those formats. Any of the volume or model formats can be used to represent segmentations.

https://www.slicer.org/wiki/Documentation/4.10/SlicerApplication/SupportedDataFormat

Thank you for reply,
However, I could not import xml and rois_series segmentations into 3D Slicer. The segmentations that I want to import were created using Osirix. 3D Slicer doesn’t respond to these data. Is there any suggestions that I can implement to solve this problem.
Thank you !

Segmentation format of Osirix is really, really bad. I don’t know if the choice of proprietary file format and poor design is intentional (to lock in users so that they can only Osirix) or just for historical reasons, but anyway, the end result is that it is really hard to export the ROIs from Osirix. If you paid for Osirix then I would recommend to ask them that they provide segmentation export tools (e.g., to standard DICOM segmentation object).

There has been an attempt to write an importer module for Slicer, based on reverse engineering of native Osirix ROI files - see here: https://github.com/VASST/SlicerOsirix. @adamrankin what’s the status of this extension? What can it do and what are its limitations?

Thank you for your quick reply, I will try your suggestion to solve the problem.

SlicerOsirix extension seems to be just an empty placeholder extension.

However, I gave it a try and was able to create a simple module to import OsiriX ROI to segmentation. It will be available for download tomorrow for Slicer Preview Release, in Sandbox extension. The module name is “Import OsiriX ROI”.

image

Give it a try and let me know if it works for you.

1 Like

That is great, thank you for your help. I will try and give feedback to you :slight_smile:

1 Like

Hello Dr Lasso,
I have installed and tried your module but acceptable input data type is just *json. I tried to convert xml file to json however ‘import OsiriX ROI module’ gave an error.

Could you please upload the xml and json file to somewhere (Dropbox, OneDrive, Google drive) and post the link?

Thank you, I’ve added code to parse XML files, too. I’ve only tested it with the data set you provided. You can get it from the extension manager tomorrow or download the updated file from here.