You pretty much have to run it through to the end. You can try using mri_coreg (this is the first step of bbregister). It does not need anything but two images and will  run in  a few min.

On 3/3/2022 5:24 AM, Guillem París wrote:

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Hello,

I'm trying to run a Boundary-based registration by using bbregister. In the documentation, it is specified that the anatomical image has to be previously analysed in FreeSurfer. I assume that means to run the "recon-all" pipeline.

Now, are all the stages of "recon-all -all" needed to perform this registration? Since I am time-constrained, I would like to run as few stages as possible, so I can use bbregister.

If it matters, I'm trying to register a DWI to the same subject's T1-w.

Thank you!

Guillem

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