External Email - Use Caution
Dear Bruce Fischl, Thank you very much for your reply. I checked the effect of going down the skull and found that a large part of the skull has not been removed. The appendix contains images of skull removal. I want to know how we should handle it.
yours yujunjie ------------------ Original ------------------ From: "Bruce Fischl"fischl@nmr.mgh.harvard.edu; Date: Sun, Nov 18, 2018 00:10 AM To: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu;
Subject: Re: [Freesurfer] Modify defect failed
Hi yujunjie
the last entry in the log file is:
CORRECTING DEFECT 5 (vertices=53772, convex hull=1434, v0=15308) XL defect detected...
this is a giant defect - about 1/4 of your total surface. It means that something major went wrong - skull attached, or hemis connected or something. You should look at the rh.orig.nofix and the rh.inflated.nofix surfaces to see what it is.
cheers Bruce
On Sat, 17 Nov 2018, 1013364183 wrote:
External Email - Use CautionDear FS, I ran the recon-all command and it failed to fix it for many days when I fixed the defect. I have modified the threshold of the split algorithm. I want to know if there are other ways to fix the Its log file is in the attachment.
Thank you in advance
yours yujunjie
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi yujunjie
you need to look at the *.nofix surfaces and see where the defect is. Skull and neck being left is around isn't a problem unless they are included in the surfaces.
cheers Bruce On Sun, 18 Nov 2018, 1013364183 wrote:
External Email - Use Caution
Dear Bruce Fischl, Thank you very much for your reply. I checked the effect of going down the skull and found that a large part of the skull has not been removed. The appendix contains images of skull removal. I want to know how we should handle it.
yours yujunjie ------------------ Original ------------------ From: "Bruce Fischl"fischl@nmr.mgh.harvard.edu; Date: Sun, Nov 18, 2018 00:10 AM To: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu; Subject: Re: [Freesurfer] Modify defect failed
Hi yujunjie
the last entry in the log file is:
CORRECTING DEFECT 5 (vertices=53772, convex hull=1434, v0=15308) XL defect detected...
this is a giant defect - about 1/4 of your total surface. It means that something major went wrong - skull attached, or hemis connected or something. You should look at the rh.orig.nofix and the rh.inflated.nofix surfaces to see what it is.
cheers Bruce
On Sat, 17 Nov 2018, 1013364183 wrote:
External Email - Use Caution
Dear FS, I ran the recon-all command and it failed to fix it for many days when I fixed the defect. I have modified the threshold of the split algorithm. I want to know if there are other ways to fix the
Its
log file is in the attachment.
Thank you in advance
yours yujunjie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Bruce,
Sorry for my intromission. I am replacing the brainmask because dura mater or skull were left behind with independence of the WM and GM segmemtation. Does this is useless?
Regards, Rosalia
El dom., 18 nov. 2018 16:16, Bruce Fischl fischl@nmr.mgh.harvard.edu escribió:
Hi yujunjie
you need to look at the *.nofix surfaces and see where the defect is. Skull and neck being left is around isn't a problem unless they are included in the surfaces.
cheers Bruce On Sun, 18 Nov 2018, 1013364183 wrote:
External Email - Use CautionDear Bruce Fischl, Thank you very much for your reply. I checked the effect of going down
the skull and found that a
large part of the skull has not been removed. The appendix contains
images of skull removal. I want
to know how we should handle it.
yours yujunjie ------------------ Original ------------------ From: "Bruce Fischl"fischl@nmr.mgh.harvard.edu; Date: Sun, Nov 18, 2018 00:10 AM To: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu; Subject: Re: [Freesurfer] Modify defect failed
Hi yujunjie
the last entry in the log file is:
CORRECTING DEFECT 5 (vertices=53772, convex hull=1434, v0=15308) XL defect detected...
this is a giant defect - about 1/4 of your total surface. It means that something major went wrong - skull attached, or hemis connected or something. You should look at the rh.orig.nofix and the rh.inflated.nofix surfaces to see what it is.
cheers Bruce
On Sat, 17 Nov 2018, 1013364183 wrote:
External Email - Use Caution
Dear FS, I ran the recon-all command and it failed to fix it for many days
when I fixed the defect. I have
modified the threshold of the split algorithm. I want to know if there
are other ways to fix the
Its
log file is in the attachment.
Thank you in advance
yours yujunjie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
that should work ok. It only matter if it affects the surfaces though (or the aseg) cheers Bruce
On Sun, 18 Nov 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use Caution
Hi Bruce, Sorry for my intromission. I am replacing the brainmask because dura mater or skull were left behind with independence of the WM and GM segmemtation. Does this is useless?
Regards, Rosalia
El dom., 18 nov. 2018 16:16, Bruce Fischl fischl@nmr.mgh.harvard.edu escribió: Hi yujunjie
you need to look at the *.nofix surfaces and see where the defect is. Skull and neck being left is around isn't a problem unless they are included in the surfaces. cheers Bruce On Sun, 18 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce Fischl, > Thank you very much for your reply. I checked the effect of going down the skull and found that a > large part of the skull has not been removed. The appendix contains images of skull removal. I want > to know how we should handle it. > > yours yujunjie > ------------------ Original ------------------ > From: "Bruce Fischl"<fischl@nmr.mgh.harvard.edu>; > Date: Sun, Nov 18, 2018 00:10 AM > To: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>; > Subject: Re: [Freesurfer] Modify defect failed > > Hi yujunjie > > the last entry in the log file is: > > CORRECTING DEFECT 5 (vertices=53772, convex hull=1434, v0=15308) > XL defect detected... > > > this is a giant defect - about 1/4 of your total surface. It means that > something major went wrong - skull attached, or hemis connected or > something. You should look at the rh.orig.nofix and the > rh.inflated.nofix surfaces to see what it is. > > cheers > Bruce > > > On Sat, 17 > Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear FS, > > I ran the recon-all command and it failed to fix it for many days when I fixed the defect. I have > > modified the threshold of the split algorithm. I want to know if there are other ways to fix the > Its > > log file is in the attachment. > > > > Thank you in advance > > > > yours yujunjie > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://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
External Email - Use Caution
Hi Bruce,
Thank you a lot for your reply. How could I inspect if affects the surfaces?
Yours sincerely, Rosalia
El dom., 18 nov. 2018 16:58, Bruce Fischl fischl@nmr.mgh.harvard.edu escribió:
that should work ok. It only matter if it affects the surfaces though (or the aseg) cheers Bruce
On Sun, 18 Nov 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use CautionHi Bruce, Sorry for my intromission. I am replacing the brainmask because dura mater or skull were left
behind with independence of the
WM and GM segmemtation. Does this is useless?
Regards, Rosalia
El dom., 18 nov. 2018 16:16, Bruce Fischl fischl@nmr.mgh.harvard.edu
escribió:
Hi yujunjie you need to look at the *.nofix surfaces and see where the defectis.
Skull and neck being left is around isn't a problem unless they are included in the surfaces. cheers Bruce On Sun, 18 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce Fischl, > Thank you very much for your reply. I checked the effect ofgoing down the skull and
found that a > large part of the skull has not been removed. The appendixcontains images of skull
removal. I want > to know how we should handle it. > > yours yujunjie > ------------------ Original ------------------ > From: "Bruce Fischl"<fischl@nmr.mgh.harvard.edu>; > Date: Sun, Nov 18, 2018 00:10 AM > To: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>; > Subject: Re: [Freesurfer] Modify defect failed > > Hi yujunjie > > the last entry in the log file is: > > CORRECTING DEFECT 5 (vertices=53772, convex hull=1434, v0=15308) > XL defect detected... > > > this is a giant defect - about 1/4 of your total surface. Itmeans that
> something major went wrong - skull attached, or hemis connectedor
> something. You should look at the rh.orig.nofix and the > rh.inflated.nofix surfaces to see what it is. > > cheers > Bruce > > > On Sat, 17 > Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear FS, > > I ran the recon-all command and it failed to fix it for manydays when I fixed the
defect. I have > > modified the threshold of the split algorithm. I want to knowif there are other
ways to fix the > Its > > log file is in the attachment. > > > > Thank you in advance > > > > yours yujunjie > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
overlay the white and pial surfaces and see if the skull is included inside the pial
On Sun, 18 Nov 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use Caution
Hi Bruce, Thank you a lot for your reply. How could I inspect if affects the surfaces?
Yours sincerely, Rosalia
El dom., 18 nov. 2018 16:58, Bruce Fischl fischl@nmr.mgh.harvard.edu escribió: that should work ok. It only matter if it affects the surfaces though (or the aseg) cheers Bruce
On Sun, 18 Nov 2018, Rosalia Dacosta Aguayo wrote: > > External Email - Use Caution > > Hi Bruce, > Sorry for my intromission. > I am replacing the brainmask because dura mater or skull were left behind with independence of the > WM and GM segmemtation. Does this is useless? > > Regards, > Rosalia > > El dom., 18 nov. 2018 16:16, Bruce Fischl <fischl@nmr.mgh.harvard.edu> escribió: > Hi yujunjie > > you need to look at the *.nofix surfaces and see where the defect is. > Skull and neck being left is around isn't a problem unless they are > included in the surfaces. > > cheers > Bruce > On Sun, 18 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear Bruce Fischl, > > Thank you very much for your reply. I checked the effect of going down the skull and > found that a > > large part of the skull has not been removed. The appendix contains images of skull > removal. I want > > to know how we should handle it. > > > > yours yujunjie > > ------------------ Original ------------------ > > From: "Bruce Fischl"<fischl@nmr.mgh.harvard.edu>; > > Date: Sun, Nov 18, 2018 00:10 AM > > To: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>; > > Subject: Re: [Freesurfer] Modify defect failed > > > > Hi yujunjie > > > > the last entry in the log file is: > > > > CORRECTING DEFECT 5 (vertices=53772, convex hull=1434, v0=15308) > > XL defect detected... > > > > > > this is a giant defect - about 1/4 of your total surface. It means that > > something major went wrong - skull attached, or hemis connected or > > something. You should look at the rh.orig.nofix and the > > rh.inflated.nofix surfaces to see what it is. > > > > cheers > > Bruce > > > > > > On Sat, 17 > > Nov 2018, 1013364183 wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear FS, > > > I ran the recon-all command and it failed to fix it for many days when I fixed the > defect. I have > > > modified the threshold of the split algorithm. I want to know if there are other > ways to fix the > > Its > > > log file is in the attachment. > > > > > > Thank you in advance > > > > > > yours yujunjie > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://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 > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks for your help :) Going on with the use Free Surfer!!
Regards, Rosalia
El dom., 18 nov. 2018 17:11, Bruce Fischl fischl@nmr.mgh.harvard.edu escribió:
overlay the white and pial surfaces and see if the skull is included inside the pial
On Sun, 18 Nov 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use CautionHi Bruce, Thank you a lot for your reply. How could I inspect if affects the
surfaces?
Yours sincerely, Rosalia
El dom., 18 nov. 2018 16:58, Bruce Fischl fischl@nmr.mgh.harvard.edu
escribió:
that should work ok. It only matter if it affects the surfacesthough (or
the aseg) cheers Bruce On Sun, 18 Nov 2018, Rosalia Dacosta Aguayo wrote: > > External Email - Use Caution > > Hi Bruce, > Sorry for my intromission. > I am replacing the brainmask because dura mater or skull wereleft behind with
independence of the > WM and GM segmemtation. Does this is useless? > > Regards, > Rosalia > > El dom., 18 nov. 2018 16:16, Bruce Fischl <fischl@nmr.mgh.harvard.edu> escribió:
> Hi yujunjie > > you need to look at the *.nofix surfaces and see where thedefect is.
> Skull and neck being left is around isn't a problem unlessthey are
> included in the surfaces. > > cheers > Bruce > On Sun, 18 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear Bruce Fischl, > > Thank you very much for your reply. I checked theeffect of going down the
skull and > found that a > > large part of the skull has not been removed. Theappendix contains images of
skull > removal. I want > > to know how we should handle it. > > > > yours yujunjie > > ------------------ Original ------------------ > > From: "Bruce Fischl"<fischl@nmr.mgh.harvard.edu>; > > Date: Sun, Nov 18, 2018 00:10 AM > > To: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>;
> > Subject: Re: [Freesurfer] Modify defect failed > > > > Hi yujunjie > > > > the last entry in the log file is: > > > > CORRECTING DEFECT 5 (vertices=53772, convex hull=1434,v0=15308)
> > XL defect detected... > > > > > > this is a giant defect - about 1/4 of your totalsurface. It means that
> > something major went wrong - skull attached, or hemisconnected or
> > something. You should look at the rh.orig.nofix and the > > rh.inflated.nofix surfaces to see what it is. > > > > cheers > > Bruce > > > > > > On Sat, 17 > > Nov 2018, 1013364183 wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear FS, > > > I ran the recon-all command and it failed to fix itfor many days when I
fixed the > defect. I have > > > modified the threshold of the split algorithm. I wantto know if there are
other > ways to fix the > > Its > > > log file is in the attachment. > > > > > > Thank you in advance > > > > > > yours yujunjie > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > >https://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
> > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
ok, let us know if we can help further Bruce On Sun, 18 Nov 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use Caution
Thanks for your help :)Going on with the use Free Surfer!!
Regards, Rosalia
El dom., 18 nov. 2018 17:11, Bruce Fischl fischl@nmr.mgh.harvard.edu escribió: overlay the white and pial surfaces and see if the skull is included inside the pial
On Sun, 18 Nov 2018, Rosalia Dacosta Aguayo wrote: > > External Email - Use Caution > > Hi Bruce, > Thank you a lot for your reply. How could I inspect if affects the surfaces? > > Yours sincerely, > Rosalia > > > El dom., 18 nov. 2018 16:58, Bruce Fischl <fischl@nmr.mgh.harvard.edu> escribió: > that should work ok. It only matter if it affects the surfaces though (or > the aseg) > cheers > Bruce > > On Sun, 18 Nov 2018, Rosalia Dacosta Aguayo wrote: > > > > > External Email - Use Caution > > > > Hi Bruce, > > Sorry for my intromission. > > I am replacing the brainmask because dura mater or skull were left behind with > independence of the > > WM and GM segmemtation. Does this is useless? > > > > Regards, > > Rosalia > > > > El dom., 18 nov. 2018 16:16, Bruce Fischl <fischl@nmr.mgh.harvard.edu> escribió: > > Hi yujunjie > > > > you need to look at the *.nofix surfaces and see where the defect is. > > Skull and neck being left is around isn't a problem unless they are > > included in the surfaces. > > > > cheers > > Bruce > > On Sun, 18 Nov 2018, 1013364183 wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear Bruce Fischl, > > > Thank you very much for your reply. I checked the effect of going down the > skull and > > found that a > > > large part of the skull has not been removed. The appendix contains images of > skull > > removal. I want > > > to know how we should handle it. > > > > > > yours yujunjie > > > ------------------ Original ------------------ > > > From: "Bruce Fischl"<fischl@nmr.mgh.harvard.edu>; > > > Date: Sun, Nov 18, 2018 00:10 AM > > > To: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>; > > > Subject: Re: [Freesurfer] Modify defect failed > > > > > > Hi yujunjie > > > > > > the last entry in the log file is: > > > > > > CORRECTING DEFECT 5 (vertices=53772, convex hull=1434, v0=15308) > > > XL defect detected... > > > > > > > > > this is a giant defect - about 1/4 of your total surface. It means that > > > something major went wrong - skull attached, or hemis connected or > > > something. You should look at the rh.orig.nofix and the > > > rh.inflated.nofix surfaces to see what it is. > > > > > > cheers > > > Bruce > > > > > > > > > On Sat, 17 > > > Nov 2018, 1013364183 wrote: > > > > > > > > > > > External Email - Use Caution > > > > > > > > Dear FS, > > > > I ran the recon-all command and it failed to fix it for many days when I > fixed the > > defect. I have > > > > modified the threshold of the split algorithm. I want to know if there are > other > > ways to fix the > > > Its > > > > log file is in the attachment. > > > > > > > > Thank you in advance > > > > > > > > yours yujunjie > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://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 > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://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
freesurfer@nmr.mgh.harvard.edu
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1013364183 -
Bruce Fischl -
Rosalia Dacosta Aguayo