No, use the register.dat that you manually created as the input to bbregister with the --init-reg. You could move your register.dat to regidster.man.dat and set the output to be register.dat. doug
Joana Braga Pereira wrote: > 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 > <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto: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.gronensch...@np.unimaas.nl> > <mailto:ed.gronensch...@np.unimaas.nl > <mailto: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 > <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> > <mailto:freesurfer-requ...@nmr.mgh.harvard.edu > <mailto: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:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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 list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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 > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 > <tel:617-726-7422> > <tel: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> > 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> > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto: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> > FileDrop: 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 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
