Re: [Freesurfer] WM edit, remove GM bright rim

[Bruce Fischl]

Hi Min

unfortunately there's not much we can do as these artifacts make the gray 
matter look just like white matter. Do you see this in many subjects?



sorry
Bruce


On Thu, 17 Mar 2016, Min Liu wrote:


Dear Bruce, 
Many thanks for looking into this. I tried to post orig.mgz to the mailing
list yesterday but the email didn't get through because the file size
exceeds 1000KB.  So I screen-captured two images to showcase the overall
quality of T1 and where the problem is.  Although the bright rim doesn't
occur everywhere, it is mostly seen in the left hemisphere.  I hope there is
a way to counteract such acquisition defects.

Thanks,
Min

On Wed, Mar 16, 2016 at 6:51 PM, Bruce Fischl 
wrote:
  Hi Min

  that looks like it might be a normalization problem. Can you
  post the orig.mgz and see what it looks like? Is there a bright
  rim in it also?

  cheers
  Bruce
  On Wed, 16 Mar 2016, Min Liu wrote:

Dear Freesufer users,
We have some T1 images having a rim of bright signal
in the GM at some spots
like the one showing in the attached Figure 1.  The
WM surface goes out to
include this bright signal and the cortex ends up
artificially thin.  We
followed the standard WM edit procedure, which is to
erase the bright signal
in wm.mgz. As shown in Figure 2, the bright rim is
replaced with intensity 1
(red). However, that doesn't improve the situation. 
Does anyone know a way
to prevent the surface from going out?

Thanks,


--
Min


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--
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Re: [Freesurfer] WM edit, remove GM bright rim

[Bruce Fischl]

Hi Min

that looks like it might be a normalization problem. Can you post the 
orig.mgz and see what it looks like? Is there a bright rim in it also?


cheers
Bruce
On 
Wed, 16 Mar 2016, Min Liu wrote:



Dear Freesufer users,
We have some T1 images having a rim of bright signal in the GM at some spots
like the one showing in the attached Figure 1.  The WM surface goes out to
include this bright signal and the cortex ends up artificially thin.  We
followed the standard WM edit procedure, which is to erase the bright signal
in wm.mgz. As shown in Figure 2, the bright rim is replaced with intensity 1
(red). However, that doesn't improve the situation.  Does anyone know a way
to prevent the surface from going out?

Thanks,


--
Min

___
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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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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] WM edit, remove GM bright rim

[Min Liu]

Dear Bruce,

Many thanks for looking into this. I tried to post orig.mgz to the mailing
list yesterday but the email didn't get through because the file size
exceeds 1000KB.  So I screen-captured two images to showcase the overall
quality of T1 and where the problem is.  Although the bright rim doesn't
occur everywhere, it is mostly seen in the left hemisphere.  I hope there
is a way to counteract such acquisition defects.

Thanks,
Min

On Wed, Mar 16, 2016 at 6:51 PM, Bruce Fischl 
wrote:

> Hi Min
>
> that looks like it might be a normalization problem. Can you post the
> orig.mgz and see what it looks like? Is there a bright rim in it also?
>
> cheers
> Bruce
>
> On Wed, 16 Mar 2016, Min Liu wrote:
>
> Dear Freesufer users,
>> We have some T1 images having a rim of bright signal in the GM at some
>> spots
>> like the one showing in the attached Figure 1.  The WM surface goes out to
>> include this bright signal and the cortex ends up artificially thin.  We
>> followed the standard WM edit procedure, which is to erase the bright
>> signal
>> in wm.mgz. As shown in Figure 2, the bright rim is replaced with
>> intensity 1
>> (red). However, that doesn't improve the situation.  Does anyone know a
>> way
>> to prevent the surface from going out?
>>
>> Thanks,
>>
>>
>> --
>> Min
>>
>>
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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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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Min
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Re: [Freesurfer] WM edit, remove GM bright rim

[Min Liu]

Dear Bruce,

Thank you very much for your reply. I think we will discard these subjects
for the analyses.

Thanks,
Min

On Thu, Mar 17, 2016 at 9:53 AM, Bruce Fischl 
wrote:

> Hi Min
>
> unfortunately there's not much we can do as these artifacts make the gray
> matter look just like white matter. Do you see this in many subjects?
>
>
> sorry
> Bruce
>
>
>
> On Thu, 17 Mar 2016, Min Liu wrote:
>
> Dear Bruce,
>> Many thanks for looking into this. I tried to post orig.mgz to the mailing
>> list yesterday but the email didn't get through because the file size
>> exceeds 1000KB.  So I screen-captured two images to showcase the overall
>> quality of T1 and where the problem is.  Although the bright rim doesn't
>> occur everywhere, it is mostly seen in the left hemisphere.  I hope there
>> is
>> a way to counteract such acquisition defects.
>>
>> Thanks,
>> Min
>>
>> On Wed, Mar 16, 2016 at 6:51 PM, Bruce Fischl > >
>> wrote:
>>   Hi Min
>>
>>   that looks like it might be a normalization problem. Can you
>>   post the orig.mgz and see what it looks like? Is there a bright
>>   rim in it also?
>>
>>   cheers
>>   Bruce
>>   On Wed, 16 Mar 2016, Min Liu wrote:
>>
>> Dear Freesufer users,
>> We have some T1 images having a rim of bright signal
>> in the GM at some spots
>> like the one showing in the attached Figure 1.  The
>> WM surface goes out to
>> include this bright signal and the cortex ends up
>> artificially thin.  We
>> followed the standard WM edit procedure, which is to
>> erase the bright signal
>> in wm.mgz. As shown in Figure 2, the bright rim is
>> replaced with intensity 1
>> (red). However, that doesn't improve the situation.
>> Does anyone know a way
>> to prevent the surface from going out?
>>
>> Thanks,
>>
>>
>> --
>> Min
>>
>>
>> ___
>> 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.
>>
>>
>>
>>
>> --
>> Min
>>
>>
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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
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> properly
> dispose of the e-mail.
>
>


-- 
Min
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