Is it possible to segment MRI image and create binary image?

Sample image and/or code

I have some MRI dicom image and I want to segement and create binary mask using imagej FiJi. is it possible?

How can I do this? Please guide me.

  • Upload an original image file here directly or share via a link to a file-sharing site (such as Dropbox) – (make sure however that you are allowed to share the image data publicly under the conditions of this forum).
  • Share a minimal working example of your macro code.


  • What is the image about? Provide some background and/or a description of the image. Try to avoid field-specific “jargon”.

Analysis goals

  • What information are you interested in getting from this image?


  • What stops you from proceeding?
  • What have you tried already?
  • Have you found any related forum topics? If so, cross-link them.
  • What software packages and/or plugins have you tried?

Hello harun,
Yes, that is what Fiji/ImageJ is intended to do. Have you ever done an image analysis before?
What format is the image in? Can you supply an example image?
When we have a look at that, we can better determine how to proceed.

Hello @smith_robertj
Thanks for your response.

Here I attached an image for a look (3D MR image with single slice 3 mm thickness). Also I’m trying to extract features from binary images.
I need some guidelines.
Thanks in advance.

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Hello harun,

First I would go to the Image > Adjust > Brighten/Contrast. Use Auto, that will make you image much easier to work with.

Since I do not know what exactly it is you are looking for I just went to Process > Binary > Make Binary, then to Edit > Invert. You see the result. If you69B0941B1674444796FF878CDD582F1D.jpg can be specific on what exactly it is you wish to determine, the process can be quite involved however and easy to accomplish.

Hope this helps,


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Try the Trainable Weka Segmentation plugin. It’s easy to use and produces a plethora of features in the ARFF data file. There is also the FeatureJ plugin that is useful