Re: [Freesurfer] Editing masks

[Bruce Fischl]

Hi Joshua
The thickness isn't well defined in the hippocampus, so you don't want to use 
it there. Use volumes of the subfields instead
Cheers
Bruce



On Jun 12, 2013, at 10:35 PM, Joshua deSouza  wrote:

> Hello Bruce,
> 
> Yes, I am using the surfaces for this. I am trying to find cortical thickness 
> differences between populations. I do not think that the mask covers the 
> entire hippocampal area, just leaving out the corpus callosum. How would I 
> include these areas into the mask?
> 
> Thank you,
> 
> Joshua
> 
> On Tue, Jun 11, 2013 at 8:29 PM, Bruce Fischl  
> wrote:
> Hi Joshua
> 
> are you using the surfaces for this? If so, you shouldn't as they are 
> undefined in those regions (since they have internal laminar structure that 
> is different than what we expect). What are you trying to achieve?
> 
> cheers
> Bruce
> 
> On Tue, 11 Jun 2013, Joshua deSouza wrote:
> 
> Hello all,
> 
> I am having a problem with generating values of the vertices at the
> hippocampal area. I believe it is a masking issue as reviewing the mask
> after the glmfit analysis I see that the mask does not cover the entire
> medial region excluding the corpus callosum. Can I do anything to change the
> mask as to add deeper brain regions at the hippocampal area?
> 
> Thank you
> 
> Joshua
> 
> 
> 
> 
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Re: [Freesurfer] Editing masks

[Joshua deSouza]

Hello Bruce,

Yes, I am using the surfaces for this. I am trying to find cortical
thickness differences between populations. I do not think that the mask
covers the entire hippocampal area, just leaving out the corpus callosum.
How would I include these areas into the mask?

Thank you,

Joshua

On Tue, Jun 11, 2013 at 8:29 PM, Bruce Fischl wrote:

> Hi Joshua
>
> are you using the surfaces for this? If so, you shouldn't as they are
> undefined in those regions (since they have internal laminar structure that
> is different than what we expect). What are you trying to achieve?
>
> cheers
> Bruce
>
> On Tue, 11 Jun 2013, Joshua deSouza wrote:
>
>  Hello all,
>>
>> I am having a problem with generating values of the vertices at the
>> hippocampal area. I believe it is a masking issue as reviewing the mask
>> after the glmfit analysis I see that the mask does not cover the entire
>> medial region excluding the corpus callosum. Can I do anything to change
>> the
>> mask as to add deeper brain regions at the hippocampal area?
>>
>> Thank you
>>
>> Joshua
>>
>>
>>
>
> 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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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Editing masks

[Bruce Fischl]

Hi Joshua

are you using the surfaces for this? If so, you shouldn't as they are 
undefined in those regions (since they have internal laminar structure 
that is different than what we expect). What are you trying to achieve?

cheers
Bruce
On Tue, 11 Jun 2013, Joshua deSouza wrote:

> Hello all,
> 
> I am having a problem with generating values of the vertices at the
> hippocampal area. I believe it is a masking issue as reviewing the mask
> after the glmfit analysis I see that the mask does not cover the entire
> medial region excluding the corpus callosum. Can I do anything to change the
> mask as to add deeper brain regions at the hippocampal area?
> 
> Thank you
> 
> Joshua
> 
>
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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
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Re: [Freesurfer] editing masks

[Bruce Fischl]

Sorry, I don't understand. Where did you get the mask? Or are you trying 
to create it from scratch?

On Tue, 5 Aug 2008, Daniel H Choi wrote:


Hi,

I have a binary mask that I apply to my .mgz files. It allows me to block
everything outside of the STG as 0 and everything inside the way it is. I
was wondering though how I might go about editing the mask? I see that there
are random voxels that have been left out and I would like to fill those in.
Thanks

Dan



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