That min cost (.86) is too high for sure. My guess is that it is the fsl init. In general, bbregister is pretty insensitive to the initialization method (as long as the init does not fail), so I would not worry about some being done with coreg and some with flirt

On 3/9/17 3:40 PM, Christopher Markiewicz wrote:

Hi Doug,

This is the final line with "cost" in it:

MinCost: 0.862331 7440.183178 7411.264107 -1.819400

We're switching from FLIRT BBR (two-pass) to bbregister when there's a reconstructed subject available, so I'm using `--init-fsl` to try to minimize the differences in the pipeline in the two cases, but I can try `--init-coreg` if there's something wrong with the initialization.

Thanks,

Chris

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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