It seems that a freesurfer user just submitted a pull request yesterday that fixes this bug:

  https://github.com/freesurfer/freesurfer/pull/24

Feel free to download the fixed version:

  https://github.com/freesurfer/freesurfer/blob/dev/scripts/bbregister

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

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.