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Registration with 3DSlicer



In this entry we look at registering one scan to another from the same subject pre and post op.



There may come a time when you have multiple scans of the same subject which you want to compare to each other.  This could be a CT and an MRI or a pre and post op scan as in this example.  Since the scans were taken at different times and possibly different places they will not line up with each other when they are loaded.  Registration is the process that can find the transformation that moves one volume to line up with the other. 


The first step after loading the data is to perform an initial alignment.  If the two volumes are far apart the difference will likely be too much for the registration algorithm to properly work.  The initial alignment is done using the 'transforms' menu within 3DSlicer.  After creating a new transform pick which volume you will be moving as the other one (fixed image) will stay stationary through the whole process.  Now adjust the 3 translation and 3 rotation sliders until you get a decent alignment by eye.  It can help to center each volume first if they have a large origin offset.  Also changing the way one of the volumes is colored can make visual alignment easier.


With the two volumes roughly lined up find the BRAINS registration within the Registration group under the main menu.  Before performing the registration set the:

  • Fixed Image
  • Moving Image
  • Output Image Volume
  • Initialization Transform
  • Registration Phases, set to Rigid (6 Degrees Of Freedom).  


When you click 'Apply 'the registration will run until it finds the best match between the scans.  Registration quality is typically measured in therms of 'Mutual Information' which is basically the union between the two volumes.


Full volume rigid registration will not work for all situations such as two scans of a foot which are flexed in a different way.  Rigid registration works best when the two scans are from the same person and the volume in question doesn't change shape (such as head scans).  Other types of registration will allows the 'moving' volume to be distorted until it matches the 'fixed' volume.  This can be simple affine (scaling) all the way to template matching (warping).


Find the scans used at:





And of course

3DSlicer - https://www.slicer.org/


Recommended Comments

Hi  Mike, 

Thanks for your video. 
I am working with a slightly different case from yours: I have two MRIs which represent the same patient (in the same position); however, one image is larger than the other (it represents a larger portion of the body).

I follow the steps you suggested.

The registration works fine, but the larger MRI is cropped to a smaller image which can overlap the other MRI. This is undesired for me since I would need the extra portion of the body originally provided by my larger image. 
Could you please help me with this?


Just to help you understand, the image below shows the output of the initial (manual) alignment, where I still see the size difference between MRIs. The lower part will then be cropped when applying the General Registration (BRAIN).


Thank you! 




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Hmm its been a while since I did a registration.  First thought is to try the reverse (register small to large).  Another option would be to try to artificially make the smaller image larger by 'padding' it with black though that could throw off the registration.

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