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
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
Awesome! Thanks for your help!
Best, Feilong
On Fri, Mar 17, 2017 at 2:57 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
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.
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
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
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 greve@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.
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 mailto: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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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 greve@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 listFreesurfer@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.
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Feilong Ma -
Z K