Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Maheen Siddiqui]

It works but the magic number now is  2067208 and read_surf still does not
read it

On Mon, Feb 29, 2016 at 7:52 PM, Douglas N Greve 
wrote:

>
> try this version
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize
>
>
> On 02/23/2016 10:17 AM, Maheen Siddiqui wrote:
> > I changed the directory and it ran, but with errors. I had to change
> > the last part --surf lh.seghead --surf-smooth 10 because it does not
> > recognise --surf. When I change this to --o, it runs but with errors.
> >
> > On Tue, Feb 23, 2016 at 2:42 PM, Douglas Greve
> > > wrote:
> >
> >
> >
> > On 2/23/16 9:39 AM, Maheen Siddiqui wrote:
> >> It seems to be giving me an error and saying it cannot read the
> >> seghead.mgz file.
> > Is it in the same directory where you are running the command? If
> > so, what is the terminal output?
> >>
> >> From my earlier question; do you know how to check if lh.seghead
> >> is corrupted?
> > If you can view it in tksurfer/freeview, then it is probably not
> > corrupted. I vaguely remember that there was some problem reading
> > this file in matlab, but I don't remember every coming up with a fix
> >
> >>
> >> On Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve
> >> >
> wrote:
> >>
> >> you can try
> >>
> >> mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead
> >> --surf-smooth 10
> >>
> >>
> >>
> >>
> >> On 2/23/16 9:22 AM, Maheen Siddiqui wrote:
> >>> Is it possible to use a different function? Can I use
> >>> mri_vol2surf on the seghead.mgz file? Or do you think that
> >>> mkheadsurf is the right one to be using?
> >>>
> >>> Thanks!!
> >>>
> >>> On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve
> >>>  >>> > wrote:
> >>>
> >>> Can you load it in tksurfer or freeview?
> >>>
> >>>
> >>> On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
>  Hi FreeSurfer users,
> 
>  I have used the "mkheadsurf" command to create a head
>  surface for my subject. However when I try to use
>  "read_surf" to read the "lh.seghead" file that is
>  created, the magic number is not one that is recognised.
> 
>  Having read some previous posts/questions with similar
>  problem/error, I think the problem is probably within
>  the "lh.seghead" file. I think someone wrote that
>  incompatibility of the magic number means that the
>  surface is corrupted. Is there a way to check errors of
>  mkheadsurf? Or whether something is wrong? It looked
>  fine in freeview.
> 
>  Does anybody have any advice?
> 
>  Thanks,
> 
>  Maheen
> 
> 
>  ___
>  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
> >>>
> >>>
> >>> 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
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> >>> was sent to you in error
> >>> but does not contain patient information, please contact
> >>> the sender and properly
> >>> dispose of the e-mail.
> >>>
> >>>
> >>>
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> >>> ___
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> 
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
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> >>
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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Maheen Siddiqui]

I still get the error option --surf unkown

On Mon, Feb 29, 2016 at 7:52 PM, Douglas N Greve 
wrote:

>
> try this version
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize
>
>
> On 02/23/2016 10:17 AM, Maheen Siddiqui wrote:
> > I changed the directory and it ran, but with errors. I had to change
> > the last part --surf lh.seghead --surf-smooth 10 because it does not
> > recognise --surf. When I change this to --o, it runs but with errors.
> >
> > On Tue, Feb 23, 2016 at 2:42 PM, Douglas Greve
> > > wrote:
> >
> >
> >
> > On 2/23/16 9:39 AM, Maheen Siddiqui wrote:
> >> It seems to be giving me an error and saying it cannot read the
> >> seghead.mgz file.
> > Is it in the same directory where you are running the command? If
> > so, what is the terminal output?
> >>
> >> From my earlier question; do you know how to check if lh.seghead
> >> is corrupted?
> > If you can view it in tksurfer/freeview, then it is probably not
> > corrupted. I vaguely remember that there was some problem reading
> > this file in matlab, but I don't remember every coming up with a fix
> >
> >>
> >> On Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve
> >> >
> wrote:
> >>
> >> you can try
> >>
> >> mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead
> >> --surf-smooth 10
> >>
> >>
> >>
> >>
> >> On 2/23/16 9:22 AM, Maheen Siddiqui wrote:
> >>> Is it possible to use a different function? Can I use
> >>> mri_vol2surf on the seghead.mgz file? Or do you think that
> >>> mkheadsurf is the right one to be using?
> >>>
> >>> Thanks!!
> >>>
> >>> On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve
> >>>  >>> > wrote:
> >>>
> >>> Can you load it in tksurfer or freeview?
> >>>
> >>>
> >>> On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
>  Hi FreeSurfer users,
> 
>  I have used the "mkheadsurf" command to create a head
>  surface for my subject. However when I try to use
>  "read_surf" to read the "lh.seghead" file that is
>  created, the magic number is not one that is recognised.
> 
>  Having read some previous posts/questions with similar
>  problem/error, I think the problem is probably within
>  the "lh.seghead" file. I think someone wrote that
>  incompatibility of the magic number means that the
>  surface is corrupted. Is there a way to check errors of
>  mkheadsurf? Or whether something is wrong? It looked
>  fine in freeview.
> 
>  Does anybody have any advice?
> 
>  Thanks,
> 
>  Maheen
> 
> 
>  ___
>  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
> >>>
> >>>
> >>> 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.
> >>>
> >>>
> >>>
> >>>
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> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> 
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
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> >> Freesurfer@nmr.mgh.harvard.edu
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> >>
> >>
> >> The information in this e-mail is intended only for the
> >> person to whom it is
> >> addressed. If 

Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Douglas N Greve]

try this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize


On 02/23/2016 10:17 AM, Maheen Siddiqui wrote:
> I changed the directory and it ran, but with errors. I had to change 
> the last part --surf lh.seghead --surf-smooth 10 because it does not 
> recognise --surf. When I change this to --o, it runs but with errors.
>
> On Tue, Feb 23, 2016 at 2:42 PM, Douglas Greve 
> > wrote:
>
>
>
> On 2/23/16 9:39 AM, Maheen Siddiqui wrote:
>> It seems to be giving me an error and saying it cannot read the
>> seghead.mgz file.
> Is it in the same directory where you are running the command? If
> so, what is the terminal output?
>>
>> From my earlier question; do you know how to check if lh.seghead
>> is corrupted?
> If you can view it in tksurfer/freeview, then it is probably not
> corrupted. I vaguely remember that there was some problem reading
> this file in matlab, but I don't remember every coming up with a fix
>
>>
>> On Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve
>> > wrote:
>>
>> you can try
>>
>> mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead
>> --surf-smooth 10
>>
>>
>>
>>
>> On 2/23/16 9:22 AM, Maheen Siddiqui wrote:
>>> Is it possible to use a different function? Can I use
>>> mri_vol2surf on the seghead.mgz file? Or do you think that
>>> mkheadsurf is the right one to be using?
>>>
>>> Thanks!!
>>>
>>> On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve
>>> >> > wrote:
>>>
>>> Can you load it in tksurfer or freeview?
>>>
>>>
>>> On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
 Hi FreeSurfer users,

 I have used the "mkheadsurf" command to create a head
 surface for my subject. However when I try to use
 "read_surf" to read the "lh.seghead" file that is
 created, the magic number is not one that is recognised.

 Having read some previous posts/questions with similar
 problem/error, I think the problem is probably within
 the "lh.seghead" file. I think someone wrote that
 incompatibility of the magic number means that the
 surface is corrupted. Is there a way to check errors of
 mkheadsurf? Or whether something is wrong? It looked
 fine in freeview.

 Does anybody have any advice?

 Thanks,

 Maheen


 ___
 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
>>>
>>>
>>> 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.
>>>
>>>
>>>
>>>
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>>> Freesurfer@nmr.mgh.harvard.edu
>>> 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
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>> 
>> 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
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>> sent to you in error
>> but does not contain patient information, please contact 

Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Maheen Siddiqui]

Just FYI, I could not get this issue resolved by altering the script. I
was, however, successfully able to get the head surface mesh using the
iso2mesh toolbox, with the vol2surf function.

On Tue, Feb 23, 2016 at 2:51 PM, Bruce Fischl 
wrote:

> the magic # 16777213 means it's a quad file, not a triangle file. I still
> would have thought we could read it fine. Do you want to email us the
> surface file and someone will take a look?
>
>
> On Tue, 23 Feb 2016, Douglas Greve wrote:
>
> Can you load it in tksurfer or freeview?
>>
>> On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
>>   Hi FreeSurfer users,
>> I have used the "mkheadsurf" command to create a head surface for my
>> subject. However when I try to use "read_surf" to
>> read the "lh.seghead" file that is created, the magic number is not one
>> that is recognised.
>>
>> Having read some previous posts/questions with similar problem/error, I
>> think the problem is probably within the
>> "lh.seghead" file. I think someone wrote that incompatibility of the
>> magic number means that the surface is corrupted. Is
>> there a way to check errors of mkheadsurf? Or whether something is wrong?
>> It looked fine in freeview.
>>
>> Does anybody have any advice?
>>
>> Thanks,
>>
>> Maheen
>>
>>
>> ___
>> 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
>
>
> 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.
>
>
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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Maheen Siddiqui]

I changed the directory and it ran, but with errors. I had to change the
last part --surf lh.seghead --surf-smooth 10 because it does not recognise
--surf. When I change this to --o, it runs but with errors.

On Tue, Feb 23, 2016 at 2:42 PM, Douglas Greve 
wrote:

>
>
> On 2/23/16 9:39 AM, Maheen Siddiqui wrote:
>
> It seems to be giving me an error and saying it cannot read the
> seghead.mgz file.
>
> Is it in the same directory where you are running the command? If so, what
> is the terminal output?
>
>
> From my earlier question; do you know how to check if lh.seghead is
> corrupted?
>
> If you can view it in tksurfer/freeview, then it is probably not
> corrupted. I vaguely remember that there was some problem reading this file
> in matlab, but I don't remember every coming up with a fix
>
>
> On Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve 
> wrote:
>
>> you can try
>>
>> mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead --surf-smooth 10
>>
>>
>>
>>
>> On 2/23/16 9:22 AM, Maheen Siddiqui wrote:
>>
>> Is it possible to use a different function? Can I use mri_vol2surf on the
>> seghead.mgz file? Or do you think that mkheadsurf is the right one to be
>> using?
>>
>> Thanks!!
>>
>> On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve <
>> gr...@nmr.mgh.harvard.edu> wrote:
>>
>>> Can you load it in tksurfer or freeview?
>>>
>>>
>>> On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
>>>
>>> Hi FreeSurfer users,
>>>
>>> I have used the "mkheadsurf" command to create a head surface for my
>>> subject. However when I try to use "read_surf" to read the "lh.seghead"
>>> file that is created, the magic number is not one that is recognised.
>>>
>>> Having read some previous posts/questions with similar problem/error, I
>>> think the problem is probably within the "lh.seghead" file. I think someone
>>> wrote that incompatibility of the magic number means that the surface is
>>> corrupted. Is there a way to check errors of mkheadsurf? Or whether
>>> something is wrong? It looked fine in freeview.
>>>
>>> Does anybody have any advice?
>>>
>>> Thanks,
>>>
>>> Maheen
>>>
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@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 mailing 
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>>
>>
>>
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>>
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>> is
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>> e-mail
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>> HelpLine at
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>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
>
> ___
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>
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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Bruce Fischl]

the magic # 16777213 means it's a quad file, not a triangle file. I still 
would have thought we could read it fine. Do you want to email us the 
surface file and someone will take a look?


On Tue, 23 Feb 2016, Douglas Greve wrote:


Can you load it in tksurfer or freeview?

On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
  Hi FreeSurfer users, 
I have used the "mkheadsurf" command to create a head surface for my subject. However 
when I try to use "read_surf" to
read the "lh.seghead" file that is created, the magic number is not one that is 
recognised. 

Having read some previous posts/questions with similar problem/error, I think 
the problem is probably within the
"lh.seghead" file. I think someone wrote that incompatibility of the magic 
number means that the surface is corrupted. Is
there a way to check errors of mkheadsurf? Or whether something is wrong? It 
looked fine in freeview. 

Does anybody have any advice?

Thanks,

Maheen 


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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Douglas Greve]

On 2/23/16 9:39 AM, Maheen Siddiqui wrote:
It seems to be giving me an error and saying it cannot read the 
seghead.mgz file.
Is it in the same directory where you are running the command? If so, 
what is the terminal output?


From my earlier question; do you know how to check if lh.seghead is 
corrupted?
If you can view it in tksurfer/freeview, then it is probably not 
corrupted. I vaguely remember that there was some problem reading this 
file in matlab, but I don't remember every coming up with a fix


On Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve 
> wrote:


you can try

mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead
--surf-smooth 10




On 2/23/16 9:22 AM, Maheen Siddiqui wrote:

Is it possible to use a different function? Can I use
mri_vol2surf on the seghead.mgz file? Or do you think that
mkheadsurf is the right one to be using?

Thanks!!

On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve
> wrote:

Can you load it in tksurfer or freeview?


On 2/23/16 8:58 AM, Maheen Siddiqui wrote:

Hi FreeSurfer users,

I have used the "mkheadsurf" command to create a head
surface for my subject. However when I try to use
"read_surf" to read the "lh.seghead" file that is created,
the magic number is not one that is recognised.

Having read some previous posts/questions with similar
problem/error, I think the problem is probably within the
"lh.seghead" file. I think someone wrote that
incompatibility of the magic number means that the surface
is corrupted. Is there a way to check errors of mkheadsurf?
Or whether something is wrong? It looked fine in freeview.

Does anybody have any advice?

Thanks,

Maheen


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person to whom it is
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contains patient information, please contact the Partners
Compliance HelpLine at
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sent to you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.




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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Maheen Siddiqui]

It seems to be giving me an error and saying it cannot read the seghead.mgz
file.

>From my earlier question; do you know how to check if lh.seghead is
corrupted?

On Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve 
wrote:

> you can try
>
> mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead --surf-smooth 10
>
>
>
>
> On 2/23/16 9:22 AM, Maheen Siddiqui wrote:
>
> Is it possible to use a different function? Can I use mri_vol2surf on the
> seghead.mgz file? Or do you think that mkheadsurf is the right one to be
> using?
>
> Thanks!!
>
> On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve 
> wrote:
>
>> Can you load it in tksurfer or freeview?
>>
>>
>> On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
>>
>> Hi FreeSurfer users,
>>
>> I have used the "mkheadsurf" command to create a head surface for my
>> subject. However when I try to use "read_surf" to read the "lh.seghead"
>> file that is created, the magic number is not one that is recognised.
>>
>> Having read some previous posts/questions with similar problem/error, I
>> think the problem is probably within the "lh.seghead" file. I think someone
>> wrote that incompatibility of the magic number means that the surface is
>> corrupted. Is there a way to check errors of mkheadsurf? Or whether
>> something is wrong? It looked fine in freeview.
>>
>> Does anybody have any advice?
>>
>> Thanks,
>>
>> Maheen
>>
>>
>> ___
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>>
>>
>>
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>>
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>> 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.
>>
>>
>
>
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> is
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> e-mail
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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Douglas Greve]

you can try

mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead --surf-smooth 10



On 2/23/16 9:22 AM, Maheen Siddiqui wrote:
Is it possible to use a different function? Can I use mri_vol2surf on 
the seghead.mgz file? Or do you think that mkheadsurf is the right one 
to be using?


Thanks!!

On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve 
> wrote:


Can you load it in tksurfer or freeview?


On 2/23/16 8:58 AM, Maheen Siddiqui wrote:

Hi FreeSurfer users,

I have used the "mkheadsurf" command to create a head surface for
my subject. However when I try to use "read_surf" to read the
"lh.seghead" file that is created, the magic number is not one
that is recognised.

Having read some previous posts/questions with similar
problem/error, I think the problem is probably within the
"lh.seghead" file. I think someone wrote that incompatibility of
the magic number means that the surface is corrupted. Is there a
way to check errors of mkheadsurf? Or whether something is wrong?
It looked fine in freeview.

Does anybody have any advice?

Thanks,

Maheen


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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Maheen Siddiqui]

Is it possible to use a different function? Can I use mri_vol2surf on the
seghead.mgz file? Or do you think that mkheadsurf is the right one to be
using?

Thanks!!

On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve 
wrote:

> Can you load it in tksurfer or freeview?
>
>
> On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
>
> Hi FreeSurfer users,
>
> I have used the "mkheadsurf" command to create a head surface for my
> subject. However when I try to use "read_surf" to read the "lh.seghead"
> file that is created, the magic number is not one that is recognised.
>
> Having read some previous posts/questions with similar problem/error, I
> think the problem is probably within the "lh.seghead" file. I think someone
> wrote that incompatibility of the magic number means that the surface is
> corrupted. Is there a way to check errors of mkheadsurf? Or whether
> something is wrong? It looked fine in freeview.
>
> Does anybody have any advice?
>
> Thanks,
>
> Maheen
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
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>
>
> 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.
>
>
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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Maheen Siddiqui]

Hi,

Yes I can load it in freeview.

On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve 
wrote:

> Can you load it in tksurfer or freeview?
>
>
> On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
>
> Hi FreeSurfer users,
>
> I have used the "mkheadsurf" command to create a head surface for my
> subject. However when I try to use "read_surf" to read the "lh.seghead"
> file that is created, the magic number is not one that is recognised.
>
> Having read some previous posts/questions with similar problem/error, I
> think the problem is probably within the "lh.seghead" file. I think someone
> wrote that incompatibility of the magic number means that the surface is
> corrupted. Is there a way to check errors of mkheadsurf? Or whether
> something is wrong? It looked fine in freeview.
>
> Does anybody have any advice?
>
> Thanks,
>
> Maheen
>
>
> ___
> Freesurfer mailing 
> listfreesur...@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.
>
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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Douglas Greve]

Can you load it in tksurfer or freeview?

On 2/23/16 8:58 AM, Maheen Siddiqui wrote:

Hi FreeSurfer users,

I have used the "mkheadsurf" command to create a head surface for my 
subject. However when I try to use "read_surf" to read the 
"lh.seghead" file that is created, the magic number is not one that is 
recognised.


Having read some previous posts/questions with similar problem/error, 
I think the problem is probably within the "lh.seghead" file. I think 
someone wrote that incompatibility of the magic number means that the 
surface is corrupted. Is there a way to check errors of mkheadsurf? Or 
whether something is wrong? It looked fine in freeview.


Does anybody have any advice?

Thanks,

Maheen


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[Freesurfer] Corrupted head surface with mkheadsurf?

[Maheen Siddiqui]

Hi FreeSurfer users,

I have used the "mkheadsurf" command to create a head surface for my
subject. However when I try to use "read_surf" to read the "lh.seghead"
file that is created, the magic number is not one that is recognised.

Having read some previous posts/questions with similar problem/error, I
think the problem is probably within the "lh.seghead" file. I think someone
wrote that incompatibility of the magic number means that the surface is
corrupted. Is there a way to check errors of mkheadsurf? Or whether
something is wrong? It looked fine in freeview.

Does anybody have any advice?

Thanks,

Maheen
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