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. > >
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