Saturday, November 24, 2012

Coregistration Demonstrations

Coregistration - the alignment of two separate modalities, such as T1-weighted and T2-weighted images - is an important precursor to normalization. This is because 1) It aligns both the anatomical and functional images into the same space and orientation; and 2) Because any warps applied to the anatomical image can then be accurately applied to the functional images as well. You can create a homemade demonstration of this yourself, using nothing more than a deck of playing cards, a lemon, and a belt.

However, before doing either coregistration or normalization, often it is useful to manually set the coordinates of the anatomical image (or whichever image you will be warping to a standardized space) so that it is in as close an alignment with the template image as possible. Since the origins of both MNI and Talairach standardized spaces are located approximately at the anterior commissure, the origin of the anatomical image should be placed there as well; this provides a better starting point for the normalization process, and increases the likelihood of success. The following tutorial shows you how to do this, as well as what the anterior commissure looks like.

Once this is done, you are ready to proceed with the coregistration step. Usually the average EPI image - output from the realignment step - will be used as the source image, while the anatomical image will be used as the reference image (the image that is moved around). Then, these warps are applied to the functional images to bring everything into harmonious alignment.


  1. Hi Andy, love the videos! Tiny mistake?
    In the video you supply the average EPI as a reference image and anatomical as the source; In the paragraph right above the video you write the instructions the other way around:
    "Usually the average EPI image - output from the realignment step - will be used as the source image, while the anatomical image will be used as the reference image".
    I believe that reference should indeed be average EPI and the source - anatomical, because I came here for a quick refresher, only looked at the text and now my functional files are 4gb a pop :/

    Thanks for making the videos, they got me all through my master's degree and now I'd still be lost without them in my PhD.

    1. I'm very glad to hear that the videos have helped! And yes, you're right about what corresponds to what; I did get those switched around. Although, technically, you could make either one the reference and the other the source (but if you're getting ginormous output, you should probably stick to the other way).



  2. Dear Andy,

    Regarding the coregistration step, I was wondering how to best deal with multiple runs. I have a dataset with 6 runs, which leads to high computational demands and long processing times if each run has to be coregistered an normalized separately. Is there a more efficient way to deal with this?

    Thank you very much,


  3. Hi Andy! When I enter my anatomical as the source image and my mean EPI from realignment as the reference image, I come out with a good coregistration. However, the rest of the EPIs from the realignment stage that I enter in as "other" images to coregister are not ending up in the same space. Visually, shouldn't they be? These are the images I will carry onto further stages of analysis, so I just want to see if something is going wrong.. Thanks!

  4. Hi Andy, first of all, thank you for the great blog and for sharing your expertise. I'm having the same issue as Nancy, above. With the anatomical as the source image and the mean EPI as reference, these two files align, but the files listed under 'other' are not realigning and going forward to later stages of processing, the activation is then outside the glass brain once I arrive at the higher level analyses. Any idea why this might be happening? Thanks!

  5. Hi..Thanku for this superb video...could you please clarify my doubt??? I want to know that is it necessary that while performing co-registration the functional and anatomical images should be of same subject or can we take standard image or template of the anatomical image