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:
- bet the template image in order to select just the skull and remove the brain inside
- register the skull-stripped image and this template skull
Both of these steps are best performed using other packages:
bet is an FSL tool, there is no real equivalent in MRtrix3.
- For registration, I would recommend you use the ANTs tools, or FSL’s FLIRT tool.
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…
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