Hi Octavian

1. Not sure - you should try them. If you have reasonable surfaces I 
think bbreg lets you specify masks to ignore, which should be giant help 
in this scenario. On the other hand, mri_robust_register does this 
automatically. They are both relatively fast so why not try and see?

2. Same answer as before. mri_robust_register has flags to tell it to use 
an inter-modal similarity function, but you can also tell bbregister it is 
a T2 and it should do a good job (and implicitly register to the T1 since 
it is already aligned with the surface).

3. I'm not sure what you mean - can you explain further?

cheers
Bruce



On Sun, 
23 Feb 2020, Octavian Lie wrote:

>        External Email - Use Caution
>
> Dear All,
>
> I need to register:
> 1. T1.mgz to a T1 postresection volume (no contrast), with large
> resection. Which one should I use, mri_robust_register, or bbregister,
> if the latter, which is the better initiator (nmi, spm, fsl)?
>
> 2. T1.mgz to a 3D FLAIR SPACE sequence (outside of the flair space
> recon-all flag), which FS registration tool should I use?
>
> 3. I then need to mask the coregistered T1 postresection with a T1.mgz mask.
>
> I would appreciate commands (either names, or full command lines),
> please advise.
>
> Thank you,
> Octavian
>
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