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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