I have written code in MATLAB that will get you part way, parsing the OsiriX XML format into a set of stacked polygons. If this would be helpful to you, send me a message and I will post the code somewhere accessible.

Hi Matthias,

How are those stacked polygons represented? Is there any way to convert them into a DICOM, Nifti with the same FOV and voxel size than the original image where the ROI was drawn?

Thanks for your answer!

It would definitely be possible to convert to a binary mask in the same DICOM coordinate system and generate either DICOM or Nifti output, but that would involve some additional coding.

Hi Angel,

I used the Inria plugin createRoiMask but the obtained volume does not overlap with my mri. I have to flip the mask and then make a translation to obtain the overlap. The problem is that the translation is not the same for all the subjects. Did you find a solution?

Thanks in advance!

Angel,

The plugin by Isiria that you listed actually works fine with the most recent version of Osirix (10.0.1 for me). I was able to export all my ROIs as a mask in Analyze format without issue. Make sure that you follow the documentation closely (http://www-sop.inria.fr/asclepios/software/pluginOsirix/createROIMask.pdf)

Hei Angel,

not sure if that's still an issue but here is a way to export e.g. a .stl file: Generate your ROI, then click on ROI -> ROI Volume -> Generate Volume. A little 3D viewer pops up and from there you can export various 3D files (which you can select bottom left of that window).

Hope that helps! I just exported some .stl files today using that approach.

Daniel F Arteaga

Hi Daniel,

I have tried to install the plugin createRoIMask you mentioned in OsiriX Lite, but the plugin cann't be loaded into OsiriX Lite. Dose this plugin only work in Osirix MD which need payment?

Thanks a lot!

Angel,

The plugin by Isiria that you listed actually works fine in Osirix lite.

just follow the "Example" given in the Isiria website.

the trick is to create a folder with the MRI data in dicoms format and the related .rois_series file exactly as shown in the Isiria example. once you have created such folder, activate the plugin and it will give you an .img file which can be uploaded for instance in ImageJ containing your segmentations.

You can import Osirix ROI (xml or json) into 3D Slicer and save it as nrrd, nifti, STL, OBJ, PLY, ... or DICOM Segmentation Object or DISOM RTSTRUCT.

You need to install Sandbox extension and use "Import OsiriX ROI" module for import. For DICOM Segmentation Object, install Quantitative Reporting extension. For DICOM RTSTRUCT export, install SlicerRT extension.