Hi Doug,
As an update, --init-coreg produced essentially the same result as --init-fsl; however, that was on EPIs we've discovered were LR flipped during reconstruction, so I've switched to a different test subject for now.
Now, for --init-fsl and --init-coreg, respectively, we get:
MinCost: 0.552768 531.638763 549.553173 0.397916 MinCost: 0.552773 531.586204 549.501644 0.394639
Again, very little difference between the two cases, so that's good. I'm not really sure how to judge what a reasonable min cost is. What criteria do you use, and is there more detailed documentation somewhere?
Thanks, Chris
On Fri, Mar 10, 2017 at 10:41 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
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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