Dear FreeSurfer Developers Is it possible to correct topological defects automatically in FreeSurfer? ( not correcting manually with Recon Edit) Thank you.
Yes, that is part of the recon-all pipeline (actually we have 3 separate topology correction procedures, two for the surface and one for the volume)
cheers Bruce On Sat, 23 Sep 2017, Fereshte wrote:
Dear FreeSurfer Developers Is it possible to correct topological defects automatically in FreeSurfer? ( not correcting manually with Recon Edit) Thank you.
Where can i find the details? Thank you.
On Sat, Sep 23, 2017 at 6:59 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Yes, that is part of the recon-all pipeline (actually we have 3 separate topology correction procedures, two for the surface and one for the volume)
cheers Bruce On Sat, 23 Sep 2017, Fereshte wrote:
Dear FreeSurfer Developers Is it possible to correct topological defects
automatically in
FreeSurfer? ( not correcting manually with Recon Edit) Thank you.
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.
Segonne, F., Pacheco, J., Fischl, B., 2007. Geometrically accurate topology-correction of cortical surfaces using nonseparating loops. IEEE Trans Med Imaging 26, 518-529.
Fischl, B., Liu, A., Dale, A.M., 2001. Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex. IEEE Trans Med Imaging 20, 70-80.
Florent Ségonne,Eric GrimsonBruce Fischl, 2003. Topological Correction of Subcortical Segmentation MICCAI 2003: Medical Image Computing and Computer-Assisted Intervention - MICCAI 2003 pp 695-702
On Sat, 23 Sep 2017, Fereshte wrote:
Where can i find the details? Thank you.
On Sat, Sep 23, 2017 at 6:59 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Yes, that is part of the recon-all pipeline (actually we have 3 separate topology correction procedures, two for the surface and one for the volume)
cheers Bruce On Sat, 23 Sep 2017, Fereshte wrote: > Dear FreeSurfer Developers Is it possible to correct topological defects automatically in > FreeSurfer? ( not correcting manually with Recon Edit) > Thank you. > >_______________________________________________ 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.
Thank you. Cheers On Sat, Sep 23, 2017 at 7:13 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Segonne, F., Pacheco, J., Fischl, B., 2007. Geometrically accurate topology-correction of cortical surfaces using nonseparating loops. IEEE Trans Med Imaging 26, 518-529.
Fischl, B., Liu, A., Dale, A.M., 2001. Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex. IEEE Trans Med Imaging 20, 70-80.
Florent Ségonne,Eric GrimsonBruce Fischl, 2003. Topological Correction of Subcortical Segmentation MICCAI 2003: Medical Image Computing and Computer-Assisted Intervention - MICCAI 2003 pp 695-702
On Sat, 23 Sep 2017, Fereshte wrote:
Where can i find the details? Thank you.
On Sat, Sep 23, 2017 at 6:59 PM Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
Yes, that is part of the recon-all pipeline (actually we have 3separate
topology correction procedures, two for the surface and one for the volume) cheers Bruce On Sat, 23 Sep 2017, Fereshte wrote: > Dear FreeSurfer Developers Is it possible to correct topologicaldefects automatically
in > FreeSurfer? ( not correcting manually with Recon Edit) > Thank you. > >_______________________________________________ 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 towhom it is
addressed. If you believe this e-mail was sent to you in error andthe e-mail
contains patient information, please contact the PartnersCompliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sentto you in error
but does not contain patient information, please contact thesender and properly
dispose of the e-mail.
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.
Dear Experts, I checked the topology corrected surfaces in recon-all pipeline however i found it didn't do well as still there are many topology defects in the pial surfaces. I know how to correct them manually in freeview but are there any commands to recorrect these topological defects with for example variables ? ( shall i use mris_fix_topology or? ) Thank you.
On Sat, Sep 23, 2017 at 7:16 PM Fereshte fereshte.ramezani@gmail.com wrote:
Thank you. Cheers
On Sat, Sep 23, 2017 at 7:13 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Segonne, F., Pacheco, J., Fischl, B., 2007. Geometrically accurate topology-correction of cortical surfaces using nonseparating loops. IEEE Trans Med Imaging 26, 518-529.
Fischl, B., Liu, A., Dale, A.M., 2001. Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex. IEEE Trans Med Imaging 20, 70-80.
Florent Ségonne,Eric GrimsonBruce Fischl, 2003. Topological Correction of Subcortical Segmentation MICCAI 2003: Medical Image Computing and Computer-Assisted Intervention - MICCAI 2003 pp 695-702
On Sat, 23 Sep 2017, Fereshte wrote:
Where can i find the details? Thank you.
On Sat, Sep 23, 2017 at 6:59 PM Bruce Fischl <
fischl@nmr.mgh.harvard.edu> wrote:
Yes, that is part of the recon-all pipeline (actually we have 3separate
topology correction procedures, two for the surface and one forthe
volume) cheers Bruce On Sat, 23 Sep 2017, Fereshte wrote: > Dear FreeSurfer Developers Is it possible to correcttopological defects automatically
in > FreeSurfer? ( not correcting manually with Recon Edit) > Thank you. > >_______________________________________________ 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 towhom it is
addressed. If you believe this e-mail was sent to you in errorand the e-mail
contains patient information, please contact the PartnersCompliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sentto you in error
but does not contain patient information, please contact thesender and properly
dispose of the e-mail.
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.
why do you think there are defects? If you have run recon-all there are pretty much guaranteed not wo be any. You can't really see this visually, but mris_euler_number will tell you if there are any
cheers Bruce On Tue, 26 Sep 2017, Fereshte wrote:
Dear Experts, I checked the topology corrected surfaces in recon-all pipeline however i found it didn't do well as still there are many topology defects in the pial surfaces. I know how to correct them manually in freeview but are there any commands to recorrect these topological defects with for example variables ? ( shall i use mris_fix_topology or? ) Thank you.
On Sat, Sep 23, 2017 at 7:16 PM Fereshte fereshte.ramezani@gmail.com wrote: Thank you. Cheers
On Sat, Sep 23, 2017 at 7:13 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Segonne, F., Pacheco, J., Fischl, B., 2007. Geometrically accurate topology-correction of cortical surfaces using nonseparating loops. IEEE Trans Med Imaging 26, 518-529.
Fischl, B., Liu, A., Dale, A.M., 2001. Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex. IEEE Trans Med Imaging 20, 70-80. Florent Ségonne,Eric GrimsonBruce Fischl, 2003. Topological Correction of Subcortical Segmentation MICCAI 2003: Medical Image Computing and Computer-Assisted Intervention - MICCAI 2003 pp 695-702 On Sat, 23 Sep 2017, Fereshte wrote: > Where can i find the details? > Thank you. > > On Sat, Sep 23, 2017 at 6:59 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > Yes, that is part of the recon-all pipeline (actually we have 3 separate > topology correction procedures, two for the surface and one for the > volume) > > cheers > Bruce > On Sat, 23 Sep 2017, Fereshte wrote: > > > Dear FreeSurfer Developers Is it possible to correct topological defects automatically > in > > FreeSurfer? ( not correcting manually with Recon Edit) > > Thank you. > > > >_______________________________________________ > 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 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.
Well i think there are some by making comparisons between surfaces( pial and white) and the segmentation before topology correction ( i could see some holes still existed) . I'm going to check the mris_euler_number to see the result. Thank you. On Tue, Sep 26, 2017 at 5:30 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
why do you think there are defects? If you have run recon-all there are pretty much guaranteed not wo be any. You can't really see this visually, but mris_euler_number will tell you if there are any
cheers Bruce On Tue, 26 Sep 2017, Fereshte wrote:
Dear Experts, I checked the topology corrected surfaces in recon-all pipeline however
i found it didn't do well as
still there are many topology defects in the pial surfaces. I know how
to correct them manually in
freeview but are there any commands to recorrect these topological
defects with for example
variables ? ( shall i use mris_fix_topology or? ) Thank you.
On Sat, Sep 23, 2017 at 7:16 PM Fereshte fereshte.ramezani@gmail.com
wrote:
Thank you.Cheers
On Sat, Sep 23, 2017 at 7:13 PM Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
Segonne, F., Pacheco, J., Fischl, B., 2007. Geometrically accurate topology-correction of cortical surfaces using nonseparatingloops. IEEE
Trans Med Imaging 26, 518-529. Fischl, B., Liu, A., Dale, A.M., 2001. Automated manifold surgery: constructing geometrically accurate and topologically correctmodels of
the human cerebral cortex. IEEE Trans Med Imaging 20, 70-80. Florent Ségonne,Eric GrimsonBruce Fischl, 2003. TopologicalCorrection of
Subcortical Segmentation MICCAI 2003: Medical Image Computing and Computer-AssistedIntervention -
MICCAI 2003 pp 695-702 On Sat, 23 Sep 2017, Fereshte wrote: > Where can i find the details? > Thank you. > > On Sat, Sep 23, 2017 at 6:59 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
> Yes, that is part of the recon-all pipeline (actually wehave 3 separate
> topology correction procedures, two for the surface andone for the
> volume) > > cheers > Bruce > On Sat, 23 Sep 2017, Fereshte wrote: > > > Dear FreeSurfer Developers Is it possible to correcttopological defects
automatically > in > > FreeSurfer? ( not correcting manually with Recon Edit) > > Thank you. > > > >_______________________________________________ > 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 theperson to whom it
is > addressed. If you believe this e-mail was sent to you inerror and the
e-mail > contains patient information, please contact the PartnersCompliance
HelpLine at > http://www.partners.org/complianceline . If the e-mailwas sent to you in
error > but does not contain patient information, please contactthe 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 The information in this e-mail is intended only for the person towhom it is
addressed. If you believe this e-mail was sent to you in error andthe e-mail
contains patient information, please contact the PartnersCompliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sentto you in error
but does not contain patient information, please contact thesender and properly
dispose of the e-mail.
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
-
Bruce Fischl -
Fereshte