We have some T1 images that are kind of noisy that were acquired several years ago. We applied a noise-reduction filter (FSL's SUSAN) to the T1 images before beginning the recon-all segmentation process. Is there any reason not to do this type of smoothing before recon-all, or is there any option in the recon-all pipeline to filter noise? Is it recommended to apply a filter before recon-all in this case?
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