As I mentioned in the previous email, you should not use bbregister for this. If you are ok with a linear registration to MNI space (not very good in general), then you should work using the commands I gave in the link you presented. If you have version 6, don't use --init-fsl

On 05/04/2018 09:51 AM, Anna Mynick wrote:

Hi all,

I’m having some trouble getting an an accurate registration between an individual functional volume and MNI152 space. Presently, I’m using the commands:

bbregister --s MNI152_FS --mov volumeInFunctional  --reg mniDir/filename2mni.lta --init-fsl --bold mri_vol2vol --mov volumeInFunctional  --reg  mniDir/filename2mni.lta --fstarg --o ‘ mniDir/filename.nii --no-resample

I’ve also tried using the strategy detailed here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-October/016016.html, without much luck (the registration was very distorted).

Is there a different method for registration to MNI152  that yields more accurate results?

Thanks very much for any suggestions!

Best, Anna

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