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 <gr...@nmr.mgh.harvard.edu>
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
> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> 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
> >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
> 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
> >>> <mailto: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 list
> >>>> Freesurfer@nmr.mgh.harvard.edu
> >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >>>>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>
> >>>
> >>> ___
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> <mailto: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
> >

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 <gr...@nmr.mgh.harvard.edu>
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
> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> 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
> >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
> 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
> >>> <mailto: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 list
> >>>> Freesurfer@nmr.mgh.harvard.edu
> >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >>>>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>
> >>>
> >>> ___
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> <mailto: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-

Re: [Freesurfer] Recon-all problem

[Maheen Siddiqui]

Can't locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup 
module)

Maybe there was a step missed of the installation? If everything is installed 
properly then recon-all works perfectly. Maybe make sure everything that was 
required from installation has been done. Or try it again?

> On 28 Feb 2016, at 11:17, Mohamed Ali Bahri  wrote:
> 
> Can't locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup 
> module)

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Re: [Freesurfer] (no subject)

[Maheen Siddiqui]

Thanks very much, I'll have a look!

On Fri, Feb 26, 2016 at 4:13 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> yes, they are documented pretty extensively on our wiki
> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
>
> On Fri, 26 Feb 2016, Maheen Siddiqui wrote:
>
> Hi,
>> Thanks for your reply. I have sought advice from someone who is
>> experienced
>> in Homer2 atlas viewer.
>>
>> Is it possible to find out the the coordinate system of the T1.mgz file
>> and
>> the surface file created by FreeSurfer?
>>
>> Thanks!
>>
>> On Fri, Feb 26, 2016 at 3:36 PM, dgw <dgwake...@gmail.com> wrote:
>>   Maheen,
>>
>>   it sounds like a question that could be better answered by the
>>   Homer2 list.
>>
>>   hth
>>   d
>>
>>   On Fri, Feb 26, 2016 at 8:13 AM, Maheen Siddiqui
>>   <maheen.siddiqu...@gmail.com> wrote:
>>   > Dear FreeSurfer Users,
>>   >
>>   > I have a head surface mesh and a pial surface mesh obtained
>>   after
>>   > segmentation of a T1 MRI scan. I am going to importing these
>>   into Homer2
>>   > Atlas Viewer as subject anatomy.
>>   >
>>   > However before I can do this import successfully, I need to
>>   bring the two
>>   > meshes into the same coordinate system. At the moment they are
>>   in different
>>   > coordinate systems (as pictured) and I need to bring the pial
>>   surface mesh
>>   > into the head surface mesh. I am a little unsure how to do
>>   this.
>>   >
>>   > Does anybody have any experience with this? Or any advice on
>>   what I could do
>>   > possibly?
>>   >
>>   > Thanks,
>>   >
>>   > Maheen
>>   >
>> > ___
>> > 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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>
>
> 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
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Re: [Freesurfer] (no subject)

[Maheen Siddiqui]

Hi,

Thanks for your reply. I have sought advice from someone who is experienced
in Homer2 atlas viewer.

Is it possible to find out the the coordinate system of the T1.mgz file and
the surface file created by FreeSurfer?

Thanks!

On Fri, Feb 26, 2016 at 3:36 PM, dgw <dgwake...@gmail.com> wrote:

> Maheen,
>
> it sounds like a question that could be better answered by the Homer2 list.
>
> hth
> d
>
> On Fri, Feb 26, 2016 at 8:13 AM, Maheen Siddiqui
> <maheen.siddiqu...@gmail.com> wrote:
> > Dear FreeSurfer Users,
> >
> > I have a head surface mesh and a pial surface mesh obtained after
> > segmentation of a T1 MRI scan. I am going to importing these into Homer2
> > Atlas Viewer as subject anatomy.
> >
> > However before I can do this import successfully, I need to bring the two
> > meshes into the same coordinate system. At the moment they are in
> different
> > coordinate systems (as pictured) and I need to bring the pial surface
> mesh
> > into the head surface mesh. I am a little unsure how to do this.
> >
> > Does anybody have any experience with this? Or any advice on what I
> could do
> > possibly?
> >
> > Thanks,
> >
> > Maheen
> >
> > ___
> > 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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>
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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 <fis...@nmr.mgh.harvard.edu>
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
>>
>>
>>
>>
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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
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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 <gr...@nmr.mgh.harvard.edu>
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 <gr...@nmr.mgh.harvard.edu>
> 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>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.
>>>
>>>
>>
>>
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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
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>> 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 <gr...@nmr.mgh.harvard.edu>
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
>>
>>
>>
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
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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 <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
>
>
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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 <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
>
>
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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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[Freesurfer] Read_surf error in reading "lh.seghead" head surface created from "mkheadsurf"

[Maheen Siddiqui]

Dear FreeSurfer users,

I have used the "mkheadsurf" function to create "lh.seghead" in the surf
folder of my subject. Now I am trying to extract the vertices and faces of
"lh.seghead" in the following way:

   *[vertex_coords, faces] = read_surf('lh.seghead')*

but get an error in read_surf which is:

 *Undefined function or variable "faces".*

* Error in read_surf (line 80)*
* faces = faces+1;*

After a bit of investigation I found that the "magic" number of the file
is 16777213 while the triangle magic number is 16777214. Since these are
unequal, it doesn't go into the if statement where faces are defined.

When I try to changed the magic number manually to be the same as the
triangle magic number, I get the following error:

 *Error using reshape*
* To RESHAPE the number of elements must not change.*

* Error in read_surf (line 76)*
* faces = reshape(faces, 3, fnum)' ;*

But I don't think making this change is a good idea as it would affect the
surfaces that I try to read that DO have magic number that is actually
equal to the triangle magic number.

Does anybody know why this might be happening? Any suggestions for me to
try? The read_surf works fine when I use it for the pial surface, just not
the lh.seghead. I am using FreeSurfer version 5.3.0.

I would appreciate any advice!

Thanks,

Maheen
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[Freesurfer] FreeSurfer MRI segmentation

[Maheen Siddiqui]

Dear FreeSurfer Users,

I have a T1 weighted MRI scan and have run the recon-all command on it. For
my steps moving forward I need to have 4 layers of tissue i.e. 4
segmentation files - GM, WM, CSF and extra cerebral tissue. Which of the
outputs from recon-all will give me the segmentation? I thought at first
that brain.mgz was what I needed but having viewed brain.mgz in Freeview,
it is just the skull stripped version of the T1 scan.

Is there any document that details all the outputs of recon-all?

Many thanks for any advice I can get!

Maheen
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Re: [Freesurfer] Combining lh. and rh. surfaces

[Maheen Siddiqui]

Hi Jesu,

Thanks very much for your reply. I have downloaded SIMNIBS and will try to
use it to do this. Is there a tutorial you recommend to do this specific
thing that I have asked?

Thanks!

Maheen

On Fri, Feb 5, 2016 at 1:39 PM, Jesu Kiran Jk <jesukir...@gmail.com> wrote:

> Hi Maheen,
>
> I have been using SIMNIBS (www.simnibs.de) script for the exact same
> thing. This script gives a mesh output.
>
> Perhaps that helps,..
>
> Kind regards,
> Jesu
>
> Jesu Kiran Spurgen
> Postgraduate Student in Advanced Medical Imaging
> KU Leuven, Belgium
>
> On Fri, Feb 5, 2016 at 1:29 PM, Maheen Siddiqui <
> maheen.siddiqu...@gmail.com> wrote:
>
>>
>> Dear FreeSurfer Users,
>>
>>
>> I have been using the recon-all FreeSurfer command to reconstruct
>> surfaces from T1 weighted MRI scan. I need to import the surfaces I have
>> into Homer2 Atlas Viewer and for this I need whole surface/volume files
>> rather than the individual hemispheres. Does anybody have experience
>> combining the hemispheres?
>>
>>
>> Many thanks,
>>
>>
>> Maheen
>>
>>
>> Maheen Siddiqui
>>
>>
>>
>> BBSRC LIDo PhD Student
>>
>> Centre for Brain and Cognitive Development
>>
>> Birkbeck, University of London
>>
>> London
>>
>>
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[Freesurfer] Combining lh. and rh. surfaces

[Maheen Siddiqui]

Dear FreeSurfer Users,


I have been using the recon-all FreeSurfer command to reconstruct surfaces
from T1 weighted MRI scan. I need to import the surfaces I have into Homer2
Atlas Viewer and for this I need whole surface/volume files rather than the
individual hemispheres. Does anybody have experience combining the
hemispheres?


Many thanks,


Maheen


Maheen Siddiqui



BBSRC LIDo PhD Student

Centre for Brain and Cognitive Development

Birkbeck, University of London

London
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