DICOM Image is too dark with ITK

Question

i am trying to read an image with ITK and display with VTK.

But there is a problem that has been haunting me for quite some time.

I read the images using the classes itkGDCMImageIO and itkImageSeriesReader.

After reading, i can do two different things:

1. I can convert the ITK image to vtkImageData using itkImageToVTKImageFilter and the use vtkImageReslicer to get all three axes. Then, i use the classes vtkImageMapper, vtkActor2D, vtkRenderer and QVTKWidget to display the image.

In this case, when i display the images, there are several problems with colors. Some of them are shown very bright, others are so dark you can barely see them.

2. The second scenario is the registration pipeline. Here, i read the image as before, then use the classes shown in the ITK Software Guide chapter about registration. Then i resample the image and use the itkImageSeriesWriter.

And that's when the problem appears. After writing the image to a file, i compare this new image with the image i used as input in the XMedcon software. If the image i wrote ahs been shown too bright in my software, there no changes when i compare both of them in XMedcon. Otherwise, if the image was too dark in my software, it appears all messed up in XMedcon.

I noticed, when comparing both images (the original and the new one) that, in both cases, there are changes in modality, pixel dimensions and glmax.

I suppose the problem is with the glmax, as the major changes occur with the darker images.

I really don't know what to do. Does this have something to do with color level/window? The most strange thing is that all the images are very similar, with identical tags and only some of them display errors when shown/written.

Answer 1

I'm not familiar with the particulars of VTK/ITK specifically, but it sounds to me like the problem is more general than that. Medical images have a high dynamic range and often the images will appear very dark or very bright if the window isn't set to some appropriate range. The DICOM tags Window Center (0028, 1050) and Window Width (0028, 1051) will include some default window settings that were selected by the modality. Usually these values are reasonable, but not always. See part 3 of the DICOM standard (11_03pu.pdf is the filename) section C.11.2.1.2 for details on how raw image pixels are scaled for display. The general idea is that you'll need to apply a linear scaling to the images to get appropriate pixel values for display.

Answer 2

What pixel types do you use? In most cases, it's simpler to use a floating point type while using ITK, but raw medical images are often in short, so that could be your problem.

You should also write the image to the disk after each step (in MHD format, for example), and inspect it with a viewer that's known to work properly, such as vv (http://www.creatis.insa-lyon.fr/rio/vv). You could also post them here as well as your code for further review.

Good luck!

Answer 3

For what you describe as your first issue:

1. I can convert the ITK image to vtkImageData using itkImageToVTKImageFilter and the use vtkImageReslicer to get all three axes. Then, i use the classes vtkImageMapper, vtkActor2D, vtkRenderer and QVTKWidget to display the image.

In this case, when i display the images, there are several problems with colors. Some of them are shown very bright, others are so dark you can barely see them.

I suggest the following: Check your window/level in VTK, they probably aren't adequate to your images. If they are abdominal tomographies window = 350 level 50 should be a nice color level.