Re: [Freesurfer] Non-grey matter classified as grey matter

[Bruce Fischl]

if the FLAIR is reasonably high resolution (no voxel dimension greater 
than around 1.5mm) then you can use the -flairpial switch to recon-all


cheers
Bruce

On Mon, 
15 Jul 2013, amirhossein manzouri wrote:



Dear Bruce, Thanks again for the response. I have FLAIR images for each
subject acquired with MPRAGE/T1. I wonder in which way I can use FLAIR
images in the analyses of cortical thickness to be able to edit (subtract)
only the part of the brain which is missegmented (segmented as gray matter
where the structure is tentorium of the cerebellum) and improve
segmentation?


On Fri, Jul 12, 2013 at 6:54 PM, amirhossein manzouri
 wrote:
  Thanks a lot!


On Fri, Jul 12, 2013 at 4:15 PM, Bruce Fischl
 wrote:
  Hi Amir

  I'm not sure I understand the question. You need to
  acquire them on each subject them same way you acquire
  your MPRAGE/T1-weighted image. Andre van der Kouwe (ccd)
  has some sequences you can use on his website if you want
  guidance on parameters and such.

  cheers
  Bruce


  On Fri, 12 Jul 2013, amirhossein manzouri wrote:

Dear Bruce, 
Would you please explain how and where to
acquire FLAIR or T2 images to
solve the problem?
BR/Amir


On Thu, Jul 11, 2013 at 9:47 PM, ye tian
 wrote:
      Dear Bruce and Doug,
Thank you very much!

PS: I searched through my data folder and
didn't find T2 images. There
goes all my afternoon!

Ye


On Thu, Jul 11, 2013 at 1:29 PM, Bruce Fischl
 wrote:
      the fix is to acquire a FLAIR or T2
image. What you are
      seing is the tentorium of the cerebellum
which is very
      difficult to distinguish from cortical
gray matter on a
      T1-weighted image. If you don't have
either of those
      datasets you probably will need to do
manual editing Bruce

      On Thu, 11 Jul 2013, ye tian wrote:

            Sorry!
            The attachments are really showing
the same
            structure, but in different
            views. I have at least a hundred
slices which
            include it. Since the pial
            surface is not extending into
cerebellum,
            should I just edit brainmask.mgz?

            Is there a quicker fix to the
problem than
            manual editing?

            Thank you very much!

            Sincerely,
            Ye


            On Thu, Jul 11, 2013 at 12:30 PM,
Douglas N
            Greve
             wrote:
                  what do you mean by the
structure in the
            circle? The circles are
                  pretty big and have a lot of
WM and GM
            in them.

                  On 07/11/2013 12:55 PM, ye
tian wrote:
                  Dear Doug,

                  Thank you very much!

                  Are you basically saying
that the
            structure in the circle
                  is not part of the cortex?

                  Sincerely,
                  Ye


            On Thu, Jul 11, 2013 at 11:01 AM,
Douglas N
            Greve
            mailto:gr...@nmr.mgh.harvard.edu>>
            wrote:

                yes
                On 07/11/2013 11:22 AM, ye
tian wrote:
                > Dear Freesurfers,
                >
                > Do you think I should delete
the extra
            dura-like structure
            in the
                > attached case?
                >
                > Thank you very much!
                >
                > Sincerely,
                > Ye
                >
                >
                >
           
___
                > Freesurfer mailing list
                >
Freesurfer@nmr.mgh.harvard.edu
               

                >
           
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

                --
                Douglas N. Greve, Ph.D.
 

Re: [Freesurfer] Non-grey matter classified as grey matter

[amirhossein manzouri]

Dear Bruce, Thanks again for the response. I have FLAIR images for each
subject acquired with MPRAGE/T1. I wonder in which way I can use FLAIR
images in the analyses of cortical thickness to be able to edit (subtract)
only the part of the brain which is missegmented (segmented as gray matter
where the structure is tentorium of the cerebellum) and improve
segmentation?


On Fri, Jul 12, 2013 at 6:54 PM, amirhossein manzouri <
a.h.manzo...@gmail.com> wrote:

> Thanks a lot!
>
>
> On Fri, Jul 12, 2013 at 4:15 PM, Bruce Fischl 
> wrote:
>
>> Hi Amir
>>
>> I'm not sure I understand the question. You need to acquire them on each
>> subject them same way you acquire your MPRAGE/T1-weighted image. Andre van
>> der Kouwe (ccd) has some sequences you can use on his website if you want
>> guidance on parameters and such.
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Fri, 12 Jul 2013, amirhossein manzouri wrote:
>>
>>  Dear Bruce,
>>> Would you please explain how and where to acquire FLAIR or T2 images to
>>> solve the problem?
>>> BR/Amir
>>>
>>>
>>> On Thu, Jul 11, 2013 at 9:47 PM, ye tian  wrote:
>>>   Dear Bruce and Doug,
>>> Thank you very much!
>>>
>>> PS: I searched through my data folder and didn't find T2 images. There
>>> goes all my afternoon!
>>>
>>> Ye
>>>
>>>
>>> On Thu, Jul 11, 2013 at 1:29 PM, Bruce Fischl
>>>  wrote:
>>>   the fix is to acquire a FLAIR or T2 image. What you are
>>>   seing is the tentorium of the cerebellum which is very
>>>   difficult to distinguish from cortical gray matter on a
>>>   T1-weighted image. If you don't have either of those
>>>   datasets you probably will need to do manual editing Bruce
>>>
>>>   On Thu, 11 Jul 2013, ye tian wrote:
>>>
>>> Sorry!
>>> The attachments are really showing the same
>>> structure, but in different
>>> views. I have at least a hundred slices which
>>> include it. Since the pial
>>> surface is not extending into cerebellum,
>>> should I just edit brainmask.mgz?
>>>
>>> Is there a quicker fix to the problem than
>>> manual editing?
>>>
>>> Thank you very much!
>>>
>>> Sincerely,
>>> Ye
>>>
>>>
>>> On Thu, Jul 11, 2013 at 12:30 PM, Douglas N
>>> Greve
>>>  wrote:
>>>   what do you mean by the structure in the
>>> circle? The circles are
>>>   pretty big and have a lot of WM and GM
>>> in them.
>>>
>>>   On 07/11/2013 12:55 PM, ye tian wrote:
>>>   Dear Doug,
>>>
>>>   Thank you very much!
>>>
>>>   Are you basically saying that the
>>> structure in the circle
>>>   is not part of the cortex?
>>>
>>>   Sincerely,
>>>   Ye
>>>
>>>
>>> On Thu, Jul 11, 2013 at 11:01 AM, Douglas N
>>> Greve
>>> >> >> >>
>>> wrote:
>>>
>>> yes
>>> On 07/11/2013 11:22 AM, ye tian wrote:
>>> > Dear Freesurfers,
>>> >
>>> > Do you think I should delete the extra
>>> dura-like structure
>>> in the
>>> > attached case?
>>> >
>>> > Thank you very much!
>>> >
>>> > Sincerely,
>>> > Ye
>>> >
>>> >
>>> >
>>> __**_
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> 
>>> >> >
>>> >
>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**
>>> freesurfer
>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> >> >
>>> Phone Number: 617-724-2358
>>> 
>>> Fax: 617-726-7422 
>>>
>>> Bugs:
>>> 
>>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
>>>
>>> 
>>> 
>>> >
>>> FileDrop:
>>> 
>>> https://gate.nmr.mgh.harvard.**edu/filedrop2
>>>
>>> 
>>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>>>
>>> >> ht

Re: [Freesurfer] Non-grey matter classified as grey matter

[amirhossein manzouri]

Thanks a lot!


On Fri, Jul 12, 2013 at 4:15 PM, Bruce Fischl wrote:

> Hi Amir
>
> I'm not sure I understand the question. You need to acquire them on each
> subject them same way you acquire your MPRAGE/T1-weighted image. Andre van
> der Kouwe (ccd) has some sequences you can use on his website if you want
> guidance on parameters and such.
>
> cheers
> Bruce
>
>
>
> On Fri, 12 Jul 2013, amirhossein manzouri wrote:
>
>  Dear Bruce,
>> Would you please explain how and where to acquire FLAIR or T2 images to
>> solve the problem?
>> BR/Amir
>>
>>
>> On Thu, Jul 11, 2013 at 9:47 PM, ye tian  wrote:
>>   Dear Bruce and Doug,
>> Thank you very much!
>>
>> PS: I searched through my data folder and didn't find T2 images. There
>> goes all my afternoon!
>>
>> Ye
>>
>>
>> On Thu, Jul 11, 2013 at 1:29 PM, Bruce Fischl
>>  wrote:
>>   the fix is to acquire a FLAIR or T2 image. What you are
>>   seing is the tentorium of the cerebellum which is very
>>   difficult to distinguish from cortical gray matter on a
>>   T1-weighted image. If you don't have either of those
>>   datasets you probably will need to do manual editing Bruce
>>
>>   On Thu, 11 Jul 2013, ye tian wrote:
>>
>> Sorry!
>> The attachments are really showing the same
>> structure, but in different
>> views. I have at least a hundred slices which
>> include it. Since the pial
>> surface is not extending into cerebellum,
>> should I just edit brainmask.mgz?
>>
>> Is there a quicker fix to the problem than
>> manual editing?
>>
>> Thank you very much!
>>
>> Sincerely,
>> Ye
>>
>>
>> On Thu, Jul 11, 2013 at 12:30 PM, Douglas N
>> Greve
>>  wrote:
>>   what do you mean by the structure in the
>> circle? The circles are
>>   pretty big and have a lot of WM and GM
>> in them.
>>
>>   On 07/11/2013 12:55 PM, ye tian wrote:
>>   Dear Doug,
>>
>>   Thank you very much!
>>
>>   Are you basically saying that the
>> structure in the circle
>>   is not part of the cortex?
>>
>>   Sincerely,
>>   Ye
>>
>>
>> On Thu, Jul 11, 2013 at 11:01 AM, Douglas N
>> Greve
>> > > >>
>> wrote:
>>
>> yes
>> On 07/11/2013 11:22 AM, ye tian wrote:
>> > Dear Freesurfers,
>> >
>> > Do you think I should delete the extra
>> dura-like structure
>> in the
>> > attached case?
>> >
>> > Thank you very much!
>> >
>> > Sincerely,
>> > Ye
>> >
>> >
>> >
>> __**_
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> 
>> > >
>> >
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**
>> freesurfer 
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> > >
>> Phone Number: 617-724-2358
>> 
>> Fax: 617-726-7422 
>>
>> Bugs:
>> 
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
>>
>> 
>> 
>> >
>> FileDrop:
>> 
>> https://gate.nmr.mgh.harvard.**edu/filedrop2
>>
>> 
>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>>
>> > html >
>> Outgoing:
>>
>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
>> greve/ 
>>
>>
>> __**_
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 
>> > >
>>
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**
>> freesurfer 

Re: [Freesurfer] Non-grey matter classified as grey matter

[Bruce Fischl]

Hi Amir

I'm not sure I understand the question. You need to acquire them on each 
subject them same way you acquire your MPRAGE/T1-weighted image. Andre van 
der Kouwe (ccd) has some sequences you can use on his website if you want 
guidance on parameters and such.


cheers
Bruce


On Fri, 12 Jul 2013, amirhossein 
manzouri wrote:



Dear Bruce, 
Would you please explain how and where to acquire FLAIR or T2 images to
solve the problem?
BR/Amir


On Thu, Jul 11, 2013 at 9:47 PM, ye tian  wrote:
  Dear Bruce and Doug,
Thank you very much!

PS: I searched through my data folder and didn't find T2 images. There
goes all my afternoon!

Ye


On Thu, Jul 11, 2013 at 1:29 PM, Bruce Fischl
 wrote:
  the fix is to acquire a FLAIR or T2 image. What you are
  seing is the tentorium of the cerebellum which is very
  difficult to distinguish from cortical gray matter on a
  T1-weighted image. If you don't have either of those
  datasets you probably will need to do manual editing Bruce

  On Thu, 11 Jul 2013, ye tian wrote:

Sorry!
The attachments are really showing the same
structure, but in different
views. I have at least a hundred slices which
include it. Since the pial
surface is not extending into cerebellum,
should I just edit brainmask.mgz?

Is there a quicker fix to the problem than
manual editing?

Thank you very much!

Sincerely,
Ye


On Thu, Jul 11, 2013 at 12:30 PM, Douglas N
Greve
 wrote:
      what do you mean by the structure in the
circle? The circles are
      pretty big and have a lot of WM and GM
in them.

      On 07/11/2013 12:55 PM, ye tian wrote:
      Dear Doug,

      Thank you very much!

      Are you basically saying that the
structure in the circle
      is not part of the cortex?

      Sincerely,
      Ye


On Thu, Jul 11, 2013 at 11:01 AM, Douglas N
Greve
mailto:gr...@nmr.mgh.harvard.edu>>
wrote:

    yes
    On 07/11/2013 11:22 AM, ye tian wrote:
    > Dear Freesurfers,
    >
    > Do you think I should delete the extra
dura-like structure
in the
    > attached case?
    >
    > Thank you very much!
    >
    > Sincerely,
    > Ye
    >
    >
    >
___
    > Freesurfer mailing list
    > Freesurfer@nmr.mgh.harvard.edu
    
    >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

    --
    Douglas N. Greve, Ph.D.
    MGH-NMR Center
    gr...@nmr.mgh.harvard.edu

    Phone Number: 617-724-2358

    Fax: 617-726-7422 

    Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
   

    FileDrop:
https://gate.nmr.mgh.harvard.edu/filedrop2
   
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
   

    Outgoing:
   
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

   
___
    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.



--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Re: [Freesurfer] Non-grey matter classified as grey matter

[amirhossein manzouri]

Dear Bruce,
Would you please explain how and where to acquire FLAIR or T2 images to
solve the problem?
BR/Amir


On Thu, Jul 11, 2013 at 9:47 PM, ye tian  wrote:

> Dear Bruce and Doug,
>
> Thank you very much!
>
> PS: I searched through my data folder and didn't find T2 images. There
> goes all my afternoon!
>
> Ye
>
>
> On Thu, Jul 11, 2013 at 1:29 PM, Bruce Fischl 
> wrote:
>
>> the fix is to acquire a FLAIR or T2 image. What you are seing is the
>> tentorium of the cerebellum which is very difficult to distinguish from
>> cortical gray matter on a T1-weighted image. If you don't have either of
>> those datasets you probably will need to do manual editing Bruce
>>
>>
>> On Thu, 11 Jul 2013, ye tian wrote:
>>
>>  Sorry!
>>> The attachments are really showing the same structure, but in different
>>> views. I have at least a hundred slices which include it. Since the pial
>>> surface is not extending into cerebellum, should I just edit
>>> brainmask.mgz?
>>>
>>> Is there a quicker fix to the problem than manual editing?
>>>
>>> Thank you very much!
>>>
>>> Sincerely,
>>> Ye
>>>
>>>
>>> On Thu, Jul 11, 2013 at 12:30 PM, Douglas N Greve
>>>  wrote:
>>>   what do you mean by the structure in the circle? The circles are
>>>   pretty big and have a lot of WM and GM in them.
>>>
>>>   On 07/11/2013 12:55 PM, ye tian wrote:
>>>   Dear Doug,
>>>
>>>   Thank you very much!
>>>
>>>   Are you basically saying that the structure in the circle
>>>   is not part of the cortex?
>>>
>>>   Sincerely,
>>>   Ye
>>>
>>>
>>> On Thu, Jul 11, 2013 at 11:01 AM, Douglas N Greve
>>> >> >> >>
>>> wrote:
>>>
>>> yes
>>> On 07/11/2013 11:22 AM, ye tian wrote:
>>> > Dear Freesurfers,
>>> >
>>> > Do you think I should delete the extra dura-like structure
>>> in the
>>> > attached case?
>>> >
>>> > Thank you very much!
>>> >
>>> > Sincerely,
>>> > Ye
>>> >
>>> >
>>> > __**_
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> >> >
>>> >
>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer
>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu 
>>> >> >
>>> Phone Number: 617-724-2358 
>>> Fax: 617-726-7422 
>>>
>>> Bugs: 
>>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
>>> 
>>> 
>>> >
>>> FileDrop: 
>>> https://gate.nmr.mgh.harvard.**edu/filedrop2
>>> 
>>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>>>
>>> 
>>> >
>>> Outgoing:
>>>
>>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/
>>>
>>> __**_
>>> 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.
>>>
>>>
>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: 
>>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
>>> FileDrop: 
>>> https://gate.nmr.mgh.harvard.**edu/filedrop2
>>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>>> Outgoing:
>>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/
>>>
>>>
>>>
>>>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.h

Re: [Freesurfer] Non-grey matter classified as grey matter

[ye tian]

Dear Bruce and Doug,

Thank you very much!

PS: I searched through my data folder and didn't find T2 images. There goes
all my afternoon!

Ye


On Thu, Jul 11, 2013 at 1:29 PM, Bruce Fischl wrote:

> the fix is to acquire a FLAIR or T2 image. What you are seing is the
> tentorium of the cerebellum which is very difficult to distinguish from
> cortical gray matter on a T1-weighted image. If you don't have either of
> those datasets you probably will need to do manual editing Bruce
>
>
> On Thu, 11 Jul 2013, ye tian wrote:
>
>  Sorry!
>> The attachments are really showing the same structure, but in different
>> views. I have at least a hundred slices which include it. Since the pial
>> surface is not extending into cerebellum, should I just edit
>> brainmask.mgz?
>>
>> Is there a quicker fix to the problem than manual editing?
>>
>> Thank you very much!
>>
>> Sincerely,
>> Ye
>>
>>
>> On Thu, Jul 11, 2013 at 12:30 PM, Douglas N Greve
>>  wrote:
>>   what do you mean by the structure in the circle? The circles are
>>   pretty big and have a lot of WM and GM in them.
>>
>>   On 07/11/2013 12:55 PM, ye tian wrote:
>>   Dear Doug,
>>
>>   Thank you very much!
>>
>>   Are you basically saying that the structure in the circle
>>   is not part of the cortex?
>>
>>   Sincerely,
>>   Ye
>>
>>
>> On Thu, Jul 11, 2013 at 11:01 AM, Douglas N Greve
>> > > >>
>> wrote:
>>
>> yes
>> On 07/11/2013 11:22 AM, ye tian wrote:
>> > Dear Freesurfers,
>> >
>> > Do you think I should delete the extra dura-like structure
>> in the
>> > attached case?
>> >
>> > Thank you very much!
>> >
>> > Sincerely,
>> > Ye
>> >
>> >
>> > __**_
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > >
>> >
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu 
>> > >
>> Phone Number: 617-724-2358 
>> Fax: 617-726-7422 
>>
>> Bugs: 
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
>> 
>> 
>> >
>> FileDrop: 
>> https://gate.nmr.mgh.harvard.**edu/filedrop2
>> 
>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>>
>> 
>> >
>> Outgoing:
>>
>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/
>>
>> __**_
>> 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.
>>
>>
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: 
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
>> FileDrop: 
>> https://gate.nmr.mgh.harvard.**edu/filedrop2
>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/
>>
>>
>>
>>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Non-grey matter classified as grey matter

[Bruce Fischl]

the fix is to acquire a FLAIR or T2 image. What you are seing is the 
tentorium of the cerebellum which is very difficult to distinguish from 
cortical gray matter on a T1-weighted image. If you don't have either of 
those datasets you probably will need to do manual editing Bruce


On Thu, 11 Jul 2013, ye tian wrote:


Sorry!
The attachments are really showing the same structure, but in different
views. I have at least a hundred slices which include it. Since the pial
surface is not extending into cerebellum, should I just edit brainmask.mgz?

Is there a quicker fix to the problem than manual editing?

Thank you very much!

Sincerely,
Ye


On Thu, Jul 11, 2013 at 12:30 PM, Douglas N Greve
 wrote:
  what do you mean by the structure in the circle? The circles are
  pretty big and have a lot of WM and GM in them.

  On 07/11/2013 12:55 PM, ye tian wrote:
  Dear Doug,

  Thank you very much!

  Are you basically saying that the structure in the circle
  is not part of the cortex?

  Sincerely,
  Ye


On Thu, Jul 11, 2013 at 11:01 AM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>>
wrote:

    yes
    On 07/11/2013 11:22 AM, ye tian wrote:
    > Dear Freesurfers,
    >
    > Do you think I should delete the extra dura-like structure
in the
    > attached case?
    >
    > Thank you very much!
    >
    > Sincerely,
    > Ye
    >
    >
    > ___
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    > Freesurfer@nmr.mgh.harvard.edu
    
    >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

    --
    Douglas N. Greve, Ph.D.
    MGH-NMR Center
    gr...@nmr.mgh.harvard.edu 
    Phone Number: 617-724-2358 
    Fax: 617-726-7422 

    Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    
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    www.nmr.mgh.harvard.edu/facility/filedrop/index.html
   

    Outgoing:
   
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Non-grey matter classified as grey matter

[Douglas N Greve]

yes
On 07/11/2013 11:22 AM, ye tian wrote:
> Dear Freesurfers,
>
> Do you think I should delete the extra dura-like structure in the 
> attached case?
>
> Thank you very much!
>
> Sincerely,
> Ye
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] Non-grey matter classified as grey matter

[ye tian]

Dear Freesurfers,

Do you think I should delete the extra dura-like structure in the attached
case?

Thank you very much!

Sincerely,
Ye
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