Forgive me if this has already been mentioned but I wasn’t able to find a procedure that works with the version of Slicer I’m using (Nightly 4.11.0, 2018-11-25) Does anyone know of a way to export a DICOM directory after segmentation? I am working with a hepatic lesion CT and have segmented the lesion, liver, and ribs. I know that I can easily export all three files as a 3D model in .OBJ or .STL format and then print it. However, I was wondering if there was a way that I can export the cropped and segmented DICOM dataset from Slicer so that another person can simply view my segmentation of the lesion slice by slice via a simple DICOM viewer.
I tried right-clicking on the parent DICOM directory (in my case a cropped DICOM dataset) and selecting “Export to DICOM” but when I click “Export” I receive the error message “Error occurred in exporter”
And another random question: Is there a way to view the 3D workspace and one of the three slices (for example: Red slice and 3D side-by-side)
You can export segmentation as DICOM RTSTRUCT if you Install SlicerRT extension. If you install Reporting extension then you may export to DICOM Segmentation object.
There was an error in the image export in nightly version that I’ve fixed today, so the export should work correctly in nightly builds that you download tomorrow or later. Latest stable Slicer-4.10.0 should work as is.
I downloaded the most recent nightly build of Slicer as well as the SlicerRT extension and am still getting the same error after clicking “Export”. Is there a step in the workflow that I am missing?
It seems that the segmentation has failed to load (segmentation file was not found). Make sure you load or create a valid segmentation and try to export that.
I believe the segmentation loaded correctly. But for some reason, while performing the export it says the segmentation is not found. But when I look at the data tree, the segmentation is there. Attached is a screenshot illustrating this.
If your goal is to “view my segmentation of the lesion slice by slice via a simple DICOM viewer”, you should probably export your segmentation as a DICOM image, and not as a DICOM Segmentation or DICOM RT object. You might want to look into the “Create DICOM Series” module. Do you have more details about the specific DICOM viewer another person is going to use?
Thank you for the suggestion. Unfortunately, when I do this, I end up with a DICOM image stack of the cropped image stack I was previously working with (prior to segmentation). Is there a setting within the “Create a DICOM Series” module where I can specify my segmentations to be included in the exported DICOM image stack.
To answer your second question, I do not have more information about the DICOM viewer the other user would use. However, my understanding is that DICOM is a universal medical imaging format so in theory any program with the ability to upload a DICOM directory into it should be able to read this exported DICOM image stack.
I agree that simple 3D image volumes can be loaded by most viewers. However, I am not sure if many viewers can show the original volume with the segmentation volume overlaid.
DICOM standard is fairly universal, but it is also huge and therefore each software application implements only a tiny fraction of it. You must know in advance what are the capabilities of the program that will need to read the data and export in an appropriate format (RTSTRUCT, segmentation object, or image volume).
Ah ok I see. So even if I was able to export the DICOM image stack from my segmentation, I would still need to make sure that the program the other user is using is capable of reading it as an RTSTRUCT, segmentation object, or image volume?
