I need to use segmented images in a program that uses segmented slices in .bmp format
I can also use segmented images in DICOM format and then transform them to .bmp
what is the best way. and how to save segmented slices images in DICOM in 3d slicer. I tried but I could not.
I also had a similar problem, Currently, I am using a workaround to export the Segmentation node as DICOM series by using the Binary Labelmap option. I am not sure it’s the proper solution, but it works for me.
Solution:
Right Click the segmentation node on Data Manager → Export visible segments to Binary Labelmap
A new segmentation label will be created, if you right-click that you will get the option to export to DICOM, where you can add details and export your segment as a DICOM series.
Hope this Helps!!
Thanks for your help !
I tried this but it looks like the generated images don’t contain the segmentation.
I think I’m doing something wrong when I get to stage of export.
In “select export type” (iten 2) has “scalar volume”, “RT” and “slicer data bundle”.
The first 2 (scalar volume and RT) generated files without segmentation and the third one did not complete.
Hi,
I think there is a small misunderstanding, probably due to my lazy short explanation.
you understood the concept of the export option which I mentioned as saving the data. Pls, see the attached images for reference. It’s actually exporting the same data inside the slicer to a different format.
Hi,
I managed to save the segmented images in dicom format using the SlicerRT extension.
I followed as recommended by you
Right Click the segmentation node on Data Manager → Export visible segments to Binary Labelmap
right-click to export to DICOM, where you can add details and export your segment as a DICOM series.
Need to choose RT in “select export type” item.
But this RT only apear if SlicerRT extension is able.
Thanks for your tips!!!
Great and good explanations !!!