Open lung CT tiff files

I don’t understand … I did as you said, but it still isn’t displaying it correctly:

What do you want to see? All three planes are now visible, use the slides above each slice view to navigate different slices.
Do you want to use 3D view? If so, you will need to use the Volume Rendering module.

I do want to see the 3d view, so how would I use the volume rendering module to create it? Btw thank you guys so much for you help!

The documentation was very helpful. However, I still have some problems. Do you know what I may do to make the 3d visualization more clear?

This looks like a clinical CT scan, for which presets provided in the volume rendering module works reasonably well. Did you try chest CT? You can also use the Shift slider left and right to see if you can improve the visualization.

@Sarang_Goel please write a bit about your overall goal. You can get much more relevant answers much quicker if we know what you would like to achieve.

What anatomy and disease you are interested in? What is the clinical question you would like to get answered? What kind of visualization, processing, or analysis do you think would help you?

So I have tried chest CT, but I am continuously getting the body with the image. However, I just want the lung. If I move the slider, the body does disappear, but so does the lung, leaving only the rib cage. Do you know what may I do?

So what my goal is to have the lung displayed, while simaltaneously dispalying a series of masked images (of abnormalities). It is centered around covid-19. These masks are already created and are also in tif format.

For covid lung visualizations, lung segmentation, and volumetric analysis you can use Lung CT analyzer extension. It is a Python scripted module so you can easily extend and customize it. We can also help making improvements or adding features, just let us know what you need.

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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 won’t work, as they don’t 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 patient’s 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.