In those cases the cost of coreg is quite close to the optimal, for example, 0.366088 vs 0.366089. I guess the final results won't differ much if I used --init-coreg instead of --init-best.
Best, Feilong On Fri, Mar 17, 2017 at 10:04 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > what happened in the ones that coreg was not the best? what is the nature > of the data? > > On 3/17/17 6:39 PM, Feilong Ma wrote: > > Thanks, Doug! I've run bbregister with --init-best on my data comparing > coreg, fsl, rr, and header; most of the times the choice is coreg as you > said (59 out of 88 total runs). > > Best, > Feilong > > On Fri, Mar 17, 2017 at 4:11 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> Hi Feilong, you do not need to use --init-best with bbregister anymore. >> It automatically uses --init-coreg (a remake of the spm coreg) which is >> the best as far a I can tell >> >> >> On 03/17/2017 02:47 PM, Feilong Ma wrote: >> > Hi FreeSurfer Developers, >> > >> > I'm having trouble using bbregister with the `--init-best` flag, a >> > minimal example and error message is like this: >> > $> bbregister --s ag00 --mov data/ag00/align/raiders/run00_ref.nii.gz >> > --init-best --bold --lta data/ag00/align/raiders/run00_ref_to_anat.lta >> > ERROR: cannot spec an init method with --init-best >> > >> > It seems `InitCoreg` is set to 1 by default in the code of bbregister. >> > Therefore, when `--init-best` is also set, it would always trigger the >> > conflict detection and exit with the error message. >> > >> > Here are some related version information: >> > - FreeSurfer version: >> > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c >> > - bbregister version: $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve >> > Exp $ >> > - OS: CentOS Linux release 7.3.1611 (Core) >> > >> > Best, >> > Feilong >> > >> > >> > >> > _______________________________________________ >> > 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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