[Mristudio-users] masking

[Shaimaa Abdelsattar]

Hi DTI experts
Could you please explain the term skull stripping and its importance for data analysis

On Apr 5, 2013, at 8:03 PM, "skhekmat" <skhekmat at hotmail.com> wrote:

> Hello Susumu
> Thanks for providing suggestions, I tried to follow that, I do have some questions on that…
>  
> From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori
> Sent: Thursday, April 04, 2013 5:34 PM
> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
> Subject: Re: [Mristudio-users] masking
>  
> Hi Ned,
>  
> The simplest masking you can use is the intensity threshold.
> When you click "tensor" calculation, there is a section to define an intensity threshold. This should suppress most of the background noise floor.
> My question is, In DTI map option ( in tensor calculation) does it create and save a mask file  using threshold option 10 %) somewhere explicitly in my computer? If so, I could not find it.
>  
> More sophisticated method is to apply for skull-strip.
> You can do this at the tensor calculation by loading a masking file, again, within the tensor calculation window.
> The brain mask file should contain 1/0 information. 
>  
> Using this option,  I created a roi mask file in binary format and but unable to load at tensor calculation, may be it reads only rec file
> Or, you can skull-strip after tensor calculation.
>  
> Using this, is a better option, after tensor calculation, I do not know how to apply to resultant images.
> For the skull-strip, you can use any software out there. We use our own skull-strip function in RoiEditor.
> You can load FA, trace, and other images with b0 or iDWI (the sum of all DWIs you can calculate in DtiStudi).
>  
> You can use b0 or iDWI for skull stripping and the resultant masking is applied to all loaded images.
>  
> Hope this will help.
>  
> Susumu
>  
> 
> On Thu, Apr 4, 2013 at 12:34 PM, skhekmat <skhekmat at hotmail.com> wrote:
> Hello All
> Is there any function to create a mask in DTI studio, so that I will apply in Tensor mapping? I could create using other softwares, however, transformation causes so many issues.
> Thanks
> Ned
> 
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>  
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