Dear Jesper,
Thank you for your suggestions.
As a clarification, this step is being completed after already running eddy. From my understanding, I believe that eddy already registers the images to the first b0 image? If so, given my next steps outlined below, is this step necessary?
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My next steps after this are to average all the b0 volumes for a given subject so that I can have one b0 volume along with my other b1 and b2 image volumes for a given subject. Then, I plan to normalize b0 intensity across all subjects.
After that, I am taking two avenues: the first is following the steps outlined in TBSS. The second is to use FNIRT to register all the images to the standard space (MNI152), so I can then input the images into DKE to get tractography maps that, when outputted, can be compared between all normalized subjects.
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Thanks,
Michael
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