The results are looking okay, however it keeps capturing other things, such as the space outside the lungs. Do you know how I may stop this?
I may also be worth to note that even if I placed more markers, this still occurs. In the video, they used a dicom file, while I am using a volume of tif files, so that may have something to do with the problem.
Voxel values in your image is not in Hounsfield units. You need to adjust the lungs threshold range in the advanced section at the bottom.
I would strongly recommend to use DICOM files as inputs, as in consumer file formats, such as TIFF you lose lots of important metadata, such as image geometry (origin, spacing, axis directions) and even image intensity values may be corrupted (as it happens in your case, too).
So even after fixing the HU values and the range, none of the results really changed. I do think my TIFF files may not be appropriate for all this. However, thank you all for your help and support!
You could try to import the lung CT as DICOM files, not as individual TIFF files. Have a look at the CTChest demo dataset (DICOM) available in slicer. This is what you would need. Try to get your own CT data sets as they would be written on a CD (DICOM) from the radiology department. Import such a CD into slicer. Then run Lung CT Analyzer. If you need help please let us know.
How did you fix the HU values?
Can you upload your scene saved as .mrb file somewhere so that we can have a look and tell what is the problem?
I basically opened my image as a python array and print the min and max HU values, and set them on the slider. I really do think the tiff files wonât work, as they donât even produce proper images of the other views (other than axial). However, this was a publically available dataset, and dicom files for covid19 arent available as they are a intrusion of the patientâs privacy (because of their metadata, etc.) I think it will be fine, but thank you all for your help!
You need to set the lung intensity range on the sliders, not the intensity range of the entire volume. You can find out the desired range easily using Threshold effect in Segment Editor module. Anyway, you can use the COVID sample data set in Sample Data module.
Ok i did this and it worked! Now i am just wondering how I can display another series of tiff files that I have (that outline the abnormalities) and overlay it with this 3d model.
If the other series contains discrete label values then load it as a labelmap volume. After loading, apply the same spacing correction as you did for the CT image.
If you work with medical images, especially 3D, then I would recommend to use nrrd file format, as it can store all essential metadata.