External Email - Use Caution
Dear FreeSurfer team,
I Have run -autorecon1 in my sample and the report.log was "finished without errors" Now, running recon-all -all I have seen that a participant is stuck in CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) for more than an hour. I wonder if this is normal or if I should be worried because recon-all takes 4.5 hours approximately for every participant but for this one, it seems that is not moving from this step.
Anyone could help me with this?
Best regards, Rosaila
Hi Rosaila
usually when you have a defect that large (>30,000) vertices, which is about 1/4 of the total surface more or less, something is dramatically wrong and it is not worth waiting for it to finish (it might take days or weeks). Examine the ?h.orig.nofix and ?h.inflated.nofix surfaces and see if there is some big problem like skull or cerebellum attached to the surface.
cheers Bruce
On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use Caution
Dear FreeSurfer team,
I Have run -autorecon1 in my sample and the report.log was "finished without errors" Now, running recon-all -all I have seen that a participant is stuck in CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) for more than an hour. I wonder if this is normal or if I should be worried because recon-all takes 4.5 hours approximately for every participant but for this one, it seems that is not moving from this step.
Anyone could help me with this?
Best regards, Rosaila
External Email - Use Caution
Hi all,
I have a stroke brain with a large lesion that runs into this same problem. Is there a way to push the process along? No white matter segmentations are created to try and edit the surface.
Best, -Lisa Krishnamurthy
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, October 22, 2018 3:30 PM To: Freesurfer support list Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT"
Hi Rosaila
usually when you have a defect that large (>30,000) vertices, which is about 1/4 of the total surface more or less, something is dramatically wrong and it is not worth waiting for it to finish (it might take days or weeks). Examine the ?h.orig.nofix and ?h.inflated.nofix surfaces and see if there is some big problem like skull or cerebellum attached to the surface.
cheers Bruce
On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use Caution
Dear FreeSurfer team,
I Have run -autorecon1 in my sample and the report.log was "finished without errors" Now, running recon-all -all I have seen that a participant is stuck in CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) for more than an hour. I wonder if this is normal or if I should be worried because recon-all takes 4.5 hours approximately for every participant but for this one, it seems that is not moving from this step.
Anyone could help me with this?
Best regards, Rosaila
Hi Lisa
no, likely you have to identify and correct the source of the giant defect, typically be either fixing the skull stripping, or editing the wm.mgz or adding control points
cheers Bruce
On Mon, 22 Oct 2018, Lisa Crystal Krishnamurthy wrote:
External Email - Use CautionHi all,
I have a stroke brain with a large lesion that runs into this same problem. Is there a way to push the process along? No white matter segmentations are created to try and edit the surface.
Best, -Lisa Krishnamurthy
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, October 22, 2018 3:30 PM To: Freesurfer support list Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT"
Hi Rosaila
usually when you have a defect that large (>30,000) vertices, which is about 1/4 of the total surface more or less, something is dramatically wrong and it is not worth waiting for it to finish (it might take days or weeks). Examine the ?h.orig.nofix and ?h.inflated.nofix surfaces and see if there is some big problem like skull or cerebellum attached to the surface.
cheers Bruce
On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use Caution
Dear FreeSurfer team,
I Have run -autorecon1 in my sample and the report.log was "finished without errors" Now, running recon-all -all I have seen that a participant is stuck in CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) for more than an hour. I wonder if this is normal or if I should be worried because recon-all takes 4.5 hours approximately for every participant but for this one, it seems that is not moving from this step.
Anyone could help me with this?
Best regards, Rosaila
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 for the quick reply! Are there online tutorials that could show me how to implement your suggestions?
Best, -Lisa
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, October 22, 2018 3:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT"
Hi Lisa
no, likely you have to identify and correct the source of the giant defect, typically be either fixing the skull stripping, or editing the wm.mgz or adding control points
cheers Bruce
On Mon, 22 Oct 2018, Lisa Crystal Krishnamurthy wrote:
External Email - Use CautionHi all,
I have a stroke brain with a large lesion that runs into this same problem. Is there a way to push the process along? No white matter segmentations are created to try and edit the surface.
Best, -Lisa Krishnamurthy
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, October 22, 2018 3:30 PM To: Freesurfer support list Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT"
Hi Rosaila
usually when you have a defect that large (>30,000) vertices, which is about 1/4 of the total surface more or less, something is dramatically wrong and it is not worth waiting for it to finish (it might take days or weeks). Examine the ?h.orig.nofix and ?h.inflated.nofix surfaces and see if there is some big problem like skull or cerebellum attached to the surface.
cheers Bruce
On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use Caution
Dear FreeSurfer team,
I Have run -autorecon1 in my sample and the report.log was "finished without errors" Now, running recon-all -all I have seen that a participant is stuck in CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) for more than an hour. I wonder if this is normal or if I should be worried because recon-all takes 4.5 hours approximately for every participant but for this one, it seems that is not moving from this step.
Anyone could help me with this?
Best regards, Rosaila
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail. nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01 %7Clkrishnamurthy%40gsu.edu%7Ca608e1a2f0964f34c96608d638558b63%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C636758337419537907&sdata=NhapXseC%2B1Hn7Yb3%2Fbyq4f1RRzKVmdB2gAfAlUPHnIQ%3D&reserved=0
External Email - Use Caution
Hi Bruce,
I cannot examine those files with gedit. Could you tell me how to open them? Thank you, Rosalia
On Mon, Oct 22, 2018 at 9:35 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Lisa
no, likely you have to identify and correct the source of the giant defect, typically be either fixing the skull stripping, or editing the wm.mgz or adding control points
cheers Bruce
On Mon, 22 Oct 2018, Lisa Crystal Krishnamurthy wrote:
External Email - Use CautionHi all,
I have a stroke brain with a large lesion that runs into this same
problem. Is there a way to push the process along? No white matter segmentations are created to try and edit the surface.
Best, -Lisa Krishnamurthy
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:
freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Monday, October 22, 2018 3:30 PM To: Freesurfer support list Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT"
Hi Rosaila
usually when you have a defect that large (>30,000) vertices, which is
about 1/4 of the total surface more or less, something is dramatically wrong and it is not worth waiting for it to finish (it might take days or weeks). Examine the ?h.orig.nofix and ?h.inflated.nofix surfaces and see if there is some big problem like skull or cerebellum attached to the surface.
cheers Bruce
On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use CautionDear FreeSurfer team,
I Have run -autorecon1 in my sample and the report.log was "finished
without errors"
Now, running recon-all -all I have seen that a participant is stuck in CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) for more than an hour. I wonder if this is normal or if I should be worried because recon-all takes 4.5 hours approximately for every participant
but for this one, it seems that is not moving from this step.
Anyone could help me with this?
Best regards, Rosaila
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
with freeview On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use Caution
Hi Bruce,
I cannot examine those files with gedit. Could you tell me how to open them? Thank you, Rosalia
On Mon, Oct 22, 2018 at 9:35 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Lisa
no, likely you have to identify and correct the source of the giant defect, typically be either fixing the skull stripping, or editing the wm.mgz or adding control points cheers Bruce On Mon, 22 Oct 2018, Lisa Crystal Krishnamurthy wrote: > External Email - Use Caution > > Hi all, > > I have a stroke brain with a large lesion that runs into this same problem. Is there a way to push the process along? No white matter segmentations are created to try and edit the surface. > > Best, > -Lisa Krishnamurthy > > -----Original Message----- > From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Monday, October 22, 2018 3:30 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT" > > Hi Rosaila > > usually when you have a defect that large (>30,000) vertices, which is about 1/4 of the total surface more or less, something is dramatically wrong and it is not worth waiting for it to finish (it might take days or weeks). Examine the ?h.orig.nofix and ?h.inflated.nofix surfaces and see if there is some big problem like skull or cerebellum attached to the surface. > > cheers > Bruce > > > On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote: > >> >> External Email - Use Caution >> >> Dear FreeSurfer team, >> >> I Have run -autorecon1 in my sample and the report.log was "finished without errors" >> Now, running recon-all -all I have seen that a participant is stuck in >> CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) for more >> than an hour. I wonder if this is normal or if I should be worried >> because recon-all takes 4.5 hours approximately for every participant but for this one, it seems that is not moving from this step. >> >> Anyone could help me with this? >> >> Best regards, >> Rosaila >> >> >> >> > > _______________________________________________ > 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
I tried. I cannot open them. They are not .mgz files, they are binary files. I will try though, and see what is happening.
Thank you, Rosalia
El lun., 22 oct. 2018 21:49, Bruce Fischl fischl@nmr.mgh.harvard.edu escribió:
with freeview On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use CautionHi Bruce,
I cannot examine those files with gedit. Could you tell me how to open
them?
Thank you, Rosalia
On Mon, Oct 22, 2018 at 9:35 PM Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
Hi Lisa no, likely you have to identify and correct the source of thegiant defect,
typically be either fixing the skull stripping, or editing thewm.mgz or
adding control points cheers Bruce On Mon, 22 Oct 2018, Lisa Crystal Krishnamurthy wrote: > External Email - Use Caution > > Hi all, > > I have a stroke brain with a large lesion that runs into thissame problem. Is there a
way to push the process along? No white matter segmentations arecreated to try and edit
the surface. > > Best, > -Lisa Krishnamurthy > > -----Original Message----- > From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf OfBruce Fischl
> Sent: Monday, October 22, 2018 3:30 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT" > > Hi Rosaila > > usually when you have a defect that large (>30,000) vertices,which is about 1/4 of
the total surface more or less, something is dramatically wrongand it is not worth
waiting for it to finish (it might take days or weeks). Examinethe ?h.orig.nofix and
?h.inflated.nofix surfaces and see if there is some big problemlike skull or cerebellum
attached to the surface. > > cheers > Bruce > > > On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote: > >> >> External Email - Use Caution >> >> Dear FreeSurfer team, >> >> I Have run -autorecon1 in my sample and the report.log was"finished without errors"
>> Now, running recon-all -all I have seen that a participant isstuck in
>> CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0)for more
>> than an hour. I wonder if this is normal or if I should beworried
>> because recon-all takes 4.5 hours approximately for everyparticipant but for this
one, it seems that is not moving from this step. >> >> Anyone could help me with this? >> >> Best regards, >> Rosaila >> >> >> >> > > _______________________________________________ > 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
yes, they are surfaces. You need to specify -f on the command line before listing the surfaces you want to load On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use Caution
I tried. I cannot open them. They are not .mgz files, they are binary files.I will try though, and see what is happening.
Thank you, Rosalia
El lun., 22 oct. 2018 21:49, Bruce Fischl fischl@nmr.mgh.harvard.edu escribió: with freeview On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:
> > External Email - Use Caution > > Hi Bruce, > > I cannot examine those files with gedit. Could you tell me how to open them? > Thank you, > Rosalia > > On Mon, Oct 22, 2018 at 9:35 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > Hi Lisa > > no, likely you have to identify and correct the source of the giant defect, > typically be either fixing the skull stripping, or editing the wm.mgz or > adding control points > > cheers > Bruce > > > On Mon, 22 Oct 2018, Lisa Crystal Krishnamurthy wrote: > > > External Email - Use Caution > > > > Hi all, > > > > I have a stroke brain with a large lesion that runs into this same problem. Is there a > way to push the process along? No white matter segmentations are created to try and edit > the surface. > > > > Best, > > -Lisa Krishnamurthy > > > > -----Original Message----- > > From: freesurfer-bounces@nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > > Sent: Monday, October 22, 2018 3:30 PM > > To: Freesurfer support list > > Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT" > > > > Hi Rosaila > > > > usually when you have a defect that large (>30,000) vertices, which is about 1/4 of > the total surface more or less, something is dramatically wrong and it is not worth > waiting for it to finish (it might take days or weeks). Examine the ?h.orig.nofix and > ?h.inflated.nofix surfaces and see if there is some big problem like skull or cerebellum > attached to the surface. > > > > cheers > > Bruce > > > > > > On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote: > > > >> > >> External Email - Use Caution > >> > >> Dear FreeSurfer team, > >> > >> I Have run -autorecon1 in my sample and the report.log was "finished without errors" > >> Now, running recon-all -all I have seen that a participant is stuck in > >> CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) for more > >> than an hour. I wonder if this is normal or if I should be worried > >> because recon-all takes 4.5 hours approximately for every participant but for this > one, it seems that is not moving from this step. > >> > >> Anyone could help me with this? > >> > >> Best regards, > >> Rosaila > >> > >> > >> > >> > > > > _______________________________________________ > > 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
I don't want to be part of this mailing list.
Thanks in advance.
freesurfer@nmr.mgh.harvard.edu
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Saturne Fox