I am trying to convert dicom CT images of brain to nii but the result of the conversion is a plain brain images where the details of the images (such as ventricles and grey matters) are all grayed out/hidden. I have attached a screenshot of a slice of the original DICOM image and the converted nii image.

But, when I adjust the window/level value of the converted nii image the details of the image are visible again. I think the conversion is not considering window width and window center value present in DICOM tags of the original dcm images.

How can I include the window width and window center for the conversion?

Thanks!

Your image has far more dynamic range than the screen. Set the image intensity minimum and maximum to highlight the tissues you are interested in. CT scans are saved as Hounsfield units, with the intensity of air very dark (-1000), soft-tissue and water in the range 0-50 and bone very bright (+1000). On option is to just set the "min" and "max" values for the window values you desire. Alternatively, right-drag your mouse over the area of the image you are interested in and it will adjust the contrast to what you are interested in. 

If you are using [MRIcroGL](https://www.nitrc.org/plugins/mwiki/inde...) you can select one of the "CT" color schemes. The image below shows the CT_Abdo scan that comes with MRIcroGL (File/OpenStandard/CTAbdo) with both the initial intensity range and with the "CT_Kidneys" color scheme applied. Choose Scripting/Templates/ct_abdomen for a graphical demonstration.

Thank You for your response!