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
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