I load tif image sequence and see the images look washed out and have strange black lines for sagittal and coronal view but not on axial view on Slicer.
The tiff images look fine to me.
Has anyone seen something like this and how do you resolve it?
I have windows 10 and slice 4.10.0.
Where do the images come from? Could you please post a few screenshots?
Check the slice spacing. Incorrect spacing in Z dimension may cause flatting of the two planes.
Thank you, @lassoan for your quick reply.
Here is the screen capture. I started to think it is not Slicer or ImageJ, but it is related to something else. I use imageJ to enhance contrast for dcom image sequence and save them as tiff images. Then use 3D slicer to load these image sequence.
- These images were loaded and displayed ok before but now they have some black lines .
- New images that were processed by imagesj have color inverted and has black line like this one
Thank you, @muratmaga.
I checked the slice spacing. They look ok (1.0mm).
Could you adjust the window/level a bit so that we can see what’s in the image?
I think after I used imageJ to enhance contrast and save images as tiff, my images were corrupted somehow. I tried to use the dcom images and load on slicer, I looks perfectly fine (no black lines in the middle like these below.
1.This was preprocessed (saved as tiff image sequence) before and when loaded on Slicer, it looks like this. Image is fine, just additional black lines.
- This one was preprocessed recently (saved as tiff image sequence) and it looks like this on slicer. It looks like its rotated, and the color is reversed.
The black lines looks like beam hardening artifacts caused by very high density regions (most likely tooth fillings and/or implants).
Thank you, @lassoan. It makes sense.
I will probably just skip using imageJ for those with braces like these and use dcom image as.
ImageJ is great software but it is mainly for microscopy images. It has some very limited 3D image support but I would not recommend it for processing CT images.
I’ll keep that in mind. Thank you, @lassoan.