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!
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.
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
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)
Hi,
For sure, I believe the data is annonymized so hopefully its ok to upload here.
the link will expire…
best
Tenzin
not sure about the software which they used.
https://wiki.cancerimagingarchive.net/display/Public/LIDC-IDRI
the dataset was from here.
@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:
Dear @lassoan ,
You said need to switch to a different module. May I know which module should use to drag xml file?
It can be any module, the important thing is not to be in the DICOM module, because when you drag-and-drop files when the DICOM browser is shown and you have a mix of DICOM and non-DICOM files then I all the files may be attempted to be interpreted as DICOM.
To load OsiriX segmentation files, you can use the Import OsiriX ROI module (provided by Sandbox extension).
Dear @lassoan ,
I did. However, the file still cannot be loaded.
I did as below
The file as here: https://drive.google.com/drive/folders/1Rj5reDzavVmU3C3D0jZarqDfse9ygv-S?usp=sharing
To load OsiriX segmentation files, you can use the Import OsiriX ROI module (provided by Sandbox extension). The module experimental (not many people use OsiriX, so it is not worth a lot of time investment to polish this feature), so it does not register a reader plugin and therefore instead of drag-and-drop you need use the module’s user interface.
