Registration between skull and skull-stripped image

I am working on anonimized mri images which as been skull stripped , but, in order to do source reconstruction, I’d need to reconstruct the skull. For this purpose I have some template images, which have not been betted. I am wondering if in Mrtrix3 it is possible to do the following steps:

  1. bet the template image in order to select just the skull and remove the brain inside
  2. register the skull-stripped image and this template skull

Both of these steps are best performed using other packages:

  1. bet is an FSL tool, there is no real equivalent in MRtrix3.
  2. For registration, I would recommend you use the ANTs tools, or FSL’s FLIRT tool.
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thank you. DO you think ANT’s is also able to register one image inside another?

For the registration part, I would register your skull-stripped images to the original template (not just the skull) and apply the estimated transformation to the template skull. Should work… :crossed_fingers:

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So , you mean to register a skull-stripped brain to a non-skull stripped template with ANTs, and then use this transformation to just register the skull-stripped brain to the skull?
thank you very much