[Mristudio-users] How to use Skull Stripping in ROIEditor

[Xin Li]

Please look at the attached screen shots.

If you want to skull strip one image, choose the "Skull strip the current active image only" option.

If you want to skull strip several images, there are two methods to do it.

1. Choose the "Skull strip the loaded images using the current active image as the template" option
2. Skull strip one image. Use the mask binary file created by DiffeoMap and the threshold function to generate a roi object. Then use the mask function to apply this roi object to other loaded images.

I recommend the second method. In general, the skull stripping function of ROIEditor will yield good results for b0 images with default parameter values. My colleagues usually skull strip B0 first and then use the second method to skull strip other images, for example, T2, T1...

There are some explanation about the parameters of the skull stripping function at 
https://www.mristudio.org/wiki/faq#head-a48a884070667bf76e504e119c05a63299e56d66
Please take a look.


Xin

----- Original Message -----
From: 陳　揚 <107310 at ib.k.u-tokyo.ac.jp>
Date: Friday, December 14, 2012 4:07 am
Subject: [Mristudio-users] How to use Skull Stripping in ROIEditor
To: mristudio-users at mristudio.org


> Hi DTI experts
>  
>  
>  I would like to use the skull stripping function in ROIEditor, 
>  so that I am doing statistical processing in MATLAB environment.
>  
>  I have the human brain trace map data in analyze format made by 
> DTI-studio as following parameters:
>  256 x 256 x 40 slices, 26 image blocks (Siemens mosaic).
>  The skull is supposed to prevent the normalize processing in MATLAB.
>  
>  
>  Please help me with this.
>  I'll appreciate your help.
>  
>  Sincerely,
>  
>  *********************************************
>  Department of Integrated Biosciences
>  Graduate School of Fronteir Sciences
>  The University of Tokyo
>  5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
>  Tel.             +81 4 7136 3634            
>  
>  YO CHIN
>  Email; 107310 at ib.k.u-tokyo.ac.jp
>  *********************************************
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>  mristudio-users at mristudio.org
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