Saved dicom to nii with saveNode, changes range of intensities and image volume

Development
1

Hi,
I load a dicom series and save it as nrrd like this:

img_node = DiskSimulator.load_image(img_dcm_dir, iid)
slicer.util.saveNode(img_node, os.path.join(self.imgs_nii_dir, iid, f"{iid}.nii.gz"))

where load_image method is defined as bellow:

def load_image(img_dicom_path, img_node_name):
      originalDicomPlugins = slicer.modules.dicomPlugins
      slicer.modules.dicomPlugins = {'DICOMScalarVolumePlugin': originalDicomPlugins['DICOMScalarVolumePlugin']}
      loadedNodeIDs = []
      with DICOMUtils.TemporaryDICOMDatabase() as db:
          DICOMUtils.importDicom(img_dicom_path, db)
          patientUIDs = db.patients()
          for patientUID in patientUIDs:
              loadedNodeIDs.extend(DICOMUtils.loadPatientByUID(patientUID))
      volumeNode = slicer.mrmlScene.GetNodeByID(loadedNodeIDs[0])
      volumeNode.SetName(img_node_name)
      slicer.modules.dicomPlugins = originalDicomPlugins
      slicer.app.applicationLogic().GetInteractionNode().SetCurrentInteractionMode(slicer.vtkMRMLInteractionNode.AdjustWindowLevel)
      return volumeNode

but when I open dicom image and nii image I see the intensity ranges and volume has some differences.

Capture2
Capture21920×897 78 KB

Here I attach a more detailed statistics of the two images loaded in MevisLab:

Capture
Capture998×388 53.3 KB

I was wondering where the difference comes from? and how can I make them the same.

  • I see the nii image is saved as integer data while dicom serie has been unsigned integer data
  • Especially in the side by side view it seems like even they are not registered, as they show different views in the same slice

Best regards,
Saeed

2

You have only saved the first loaded node (loadedNodeIDs[0]) of the first patient in the database. Probably it was a different image than what you loaded manually. You can save all the loaded nodes (instead of just the first one) and then you’ll probably find the corresponding volumes.

3

Thanks Andras, I believe that’s not the case, since I printed the length of loadedNodeIDs, it just has one element in it, which is what I saved.
So I checked with exporting the loaded DICOM node in slicer UI by right clicking and “export to DICOM”.

image
image663×619 23.6 KB

when I check the exported DICOM serie with the input DICOM serie, the image data is different. I think the reason should lie in “export type” (above screenshot)? that’s the only place I see can make difference.

image
image983×309 9.42 KB

these are statistics of loaded DICOM serie and exported DICOM serie. I’m wondering what’s makes the difference? how can I avoid it?

4

You created a new topic for this, so let’s stop the discussion here and continue it there: