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> 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 > > 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 >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> 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 . 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 > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > 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 . 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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