I have a pre-determined VOI segmentation and DCE MRI sequence in DICOM format, and want to overlay/align them. What is the best way to go about this? I was thinking about converting the VOI segmentation to a labelmap volume matched to reference geometry of the DCE MRI’s. Would this work to align?
Yes, you should be able to load the segmentation as a segmentation node and the MRI as a volume node and Slicer will overlay them correctly. There are many visualization parameters that you can tune in Segmentations module’s Display section.
When I try to do this, I load the MRI as a volume using slicer.util.loadVolume(), and then want to use the code below. However, I’m not sure how to (1) get the MRML node of the loaded MRI volume and (2) load the segmentation before getting the segmentation node as below. Thanks!
I am able to load the MRI dicom’s as a volume, but I am having trouble loading the segmentation. The segmentation file is also in dicom format, so I am trying to load as labelmap through GUI following instructions (https://slicer.readthedocs.io/en/latest/user_guide/modules/segmentations.html) but I don’t see this option. What do you recommend?
Please ignore my last reply, I was able to get it to work by putting the seg files in the same folder. The new problem I have is that 2 of the segmentation files (specifically PE segmentations) are not able to load as a DICOMsegmentation-- do you know why this could be? Thanks
Luckily this worked – thank you. I have a follow - up question: to export a labelmap volume (based on the aligned MRI volume reference geometry with the segmentation file) to a file, what are the settings I should use in the segmentations module? Thank you
In general, if you don’t need any special behavior, use default settings. To set a reference geometry for export, select the reference volume in Segmentations module / Export/import… / Advanced / Reference volume.
Export/import models and labelmaps exports to nodes in the scene (that you can later save to files using Save data… window). “Export to files” saves directly to files.
@Sunderlandkyl what geometry is used by “Export to files” when exporting nrrd/nifti? Probably we should add a reference volume selector there, too.
Export to file currently uses the reference geometry string. I believe it’s the same with both export to labelmap and export to files (with the exception of the reference volume selector). I’ll add a combo box to choose the reference volume.