On Thu, Mar 9, 2017 at 3:29 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

that should have worked. what was the bbregister final cost function? It
could have been that fsl did not provide a good initial registration. If
you have v6, you can leave off --init-fsl and it will use mri_coreg
(which is more robust).

On 03/09/2017 03:24 PM, Christopher Markiewicz wrote:
> Hi all,
>
> Suppose you have a sub-pipeline:
>
> $ recon-all -s $SUBJ -i $T1 -all
> $ bbregister --s $SUBJ --mov $EPI --init-fsl --t2 --reg bbreg.dat
> --fslmat fsl.mat
>
> Now `bbreg.dat`/`fsl.mat` is registered to
> `$SUBJECTS_DIR/$SUBJ/mri/T1.mgz`; what's the best way to register to $T1?
>
> I've tried:
>
> $ tkregister2 --no-edit --mov $EPI --reg bbreg.dat --targ $T1
> --fslregout adjusted.mat
>
> And that's clearly wrong, but I'm kind of stuck on where to go from
> here. Anybody see where I'm going wrong?
>
> Thanks,
> Chris
>
>

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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