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 greve@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 < greve@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
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