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 <greve@nmr.mgh.harvard.edu mailto: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 <mailto: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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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