Hi Doug, Thanks for the reply. I'm not sure i understand how to solve it. Are you suggesting to re-run bbregister using the --init-reg option and the register.dat files that were previously created for the badly-registered subjects?
Joana 2011/10/17 Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Those almost surely failed because of a bad initialization. You can usually > tell this by looking at the first value in the mincost file. For these, the > mincost is something like .9. The mincost will be a value bet 0 and 1.1, > with 0 being perfect. Looks at your good subjects to get an idea of what > range to expect for well-registered subjects. You should be able to use the > registrations you created as input to bbregister (with the --init-reg > option), and bbregister should do fine after that. > doug > > Joana Braga Pereira wrote: > >> Hi Doug, >> >> I made quite a few changes, including translations and rotations (not >> scaling changes), to 10 out of 24 subjects. >> >> Here are a few of the bbregister log.files from subjects in which the >> registration didn't go well. >> >> Thanks for the help! >> >> Joana >> >> 2011/10/17 Douglas N Greve <gr...@nmr.mgh.harvard.edu <mailto: >> gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>> >> >> >> Hi Joana, how big were the changes that you made? Sometimes the >> initialization routine won't get it close enough, then bbregister >> fails. Can you send the bbregister log file? >> doug >> >> Lilla Zollei wrote: >> >> >> Even though it is not ideal, manual adjustments can be useful. >> I would use manual registration in a small number of cases >> though. If most of your data requires it, I would try to play >> with the automatic registration parameters more. >> >> --Lilla >> >> On Sun, 16 Oct 2011, Joana Braga Pereira wrote: >> >> Dear Lilla and Ed, >> Thanks a lot for your suggestions, they were really really >> helpful! >> >> I did the analyses as you suggested. After bbregister i >> checked the results with tkregister2 and saw that most >> subjects were well coregistered. However in a few of them >> my lowb images were out of place with respect to the >> target and so i made manual adjustments using bbregister >> interface tools.. >> >> I was just wondering whether this is the normal procedure >> as manual adjustments can be quite subjective and i would >> prefer not to introduce such a bias in the analyses. >> >> Thanks a lot for your valuable help! >> >> Joana >> >> 2011/10/15 Ed Gronenschild < >> ed.gronensch...@np.unimaas.nl >> >> <mailto:ed.gronenschild@np.**unimaas.nl<ed.gronensch...@np.unimaas.nl> >> >> >> >> Dear Joana, >> Two things: >> >> 1. >> You should be very careful to use fslswapdim since it may >> result >> in an unintended left-right flipping. It's better to use >> fslreorient2std. >> 2. >> The tool dt-recon computes the coregistration of the lowb >> volume to >> the anatomical volume, see register.dat. >> You can then use the following to coregister FA: >> >> mri_vol2vol --reg register.dat --mov fa.nii --o >> fa-ana.nii -targ subject/mri/T1.mgz >> >> where "subject" is the output folder generated by the >> recon-all command. >> You should not forget to set the global variable SUBJECTS_DIR >> >> Cheers, >> Ed >> >> On 14 Oct, 2011, at 18:00, >> >> freesurfer-requ...@nmr.mgh.**harvard.edu<freesurfer-requ...@nmr.mgh.harvard.edu> >> >> <mailto:freesurfer-request@**nmr.mgh.harvard.edu<freesurfer-requ...@nmr.mgh.harvard.edu>> >> wrote: >> >> >> Dear Bruce and Anastasia, >> >> Thanks for the quick reply! >> >> I tried the bbregister as you suggested but when i >> visualize the target and >> dti image they don't look registered at all. >> >> This is the comand i used: >> >> bbregister --s CN01 --mov >> /home/joana/FA/CN01/dti_FA.**nii.gz --reg >> /home/joana/FA/CN01/register.**dat --init-fsl --dti >> --template-out >> /home/joana/FA/CN01/template.**nii.gz --fslmat >> /home/joana/FA/CN01/flirt.tmx >> >> I tried to use the bbregister tools to align them but I >> didn't get very >> far... >> >> Did i miss something? >> >> I read in another mail something about using the >> register.dat created in >> bbregister and do mri_label2vol but i'm not sure how to do it. >> >> Thanks, >> >> Joana >> >> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<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:freesur...@nmr.mgh.**harvard.edu<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 >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@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> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> >> > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >
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