There is no way to set a hard and fast threshold. I would recommend
running a set of them (20ish), checking them manually to assure that
they are correct, then compute the mean and stddev of the mincost. For a
new data set, you can compute a z-score of the mincost and then pick a
threshold that you are comforatable with (you only have to worrry about
it when the mincost is larger than the mean)
On 3/14/17 1:29 PM, Christopher Markiewicz wrote:
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
<gr...@nmr.mgh.harvard.edu <mailto:gr...@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
<gr...@nmr.mgh.harvard.edu <mailto:gr...@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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