Dragging xml file as segmentation in 3D slicer

Support
1

I have a file with dicom images (CT volume) and xml as the segmentation (just one xml file), when I drag the whole file into the slicer, only dicom image is shown, I couldn’t get the xml segmentation to be imported.

I checked the data as well and there is only the CT volume. I would like to ask how can I import the xml file. Eventually I would like to convert it to nrrd segmentation file.

Thank you!

2

If the DICOM module is active then all drag-and-dropped file goes right into the DICOM database. If you want to load non-DICOM data, for example OsiriX segmentation files then switch to a different module before drag-and-dropping the data.

3

Hi Andras,

I did do that but didn’t work.

I have a folder that contains the CT volume and one xml file as well, I tried to drag the folder but it didnt show the segmentation, only the CT volume.

best
Tenzin

4

What software did you use for creating this segmentation?
Can you provide an example? (upload it to somewhere and post the link here; make sure no patient information is included)

5

Hi,

For sure, I believe the data is annonymized so hopefully its ok to upload here.

the link will expire…

best
Tenzin

6

not sure about the software which they used.

https://wiki.cancerimagingarchive.net/display/Public/LIDC-IDRI

the dataset was from here.

7

@tenzin_kunkyab: That data is famously hard to work with in its native form, but fortunately @fedorov has spent a lot of time making standard representations that are easy to work with in Slicer. Please read this paper for details:

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