[Mristudio-users] Mean_ADC units

Fri Mar 6 15:16:32 EST 2009

OK, here is the procedure;

1) Please prepare one FA map and one b0 (or meanDWI)

2) Load the FA map to RoiEditor using the left upper "open" icon

3) Load the b0 (or meanDWI) using the "open" icon in the right column,
"Image" section.

4) Make sure that you have FA and b0 both loaded into one window using the
pull-down menu in the "image" section

------ Skull-stripping Using b0 (or meanDWI) --------

5) Choose the b0 image as the active image.

6) Choose the "Seeded Region Growing" tool in the "Tool" section

7) Choose "absolute" and "3D" radio buttons.

8) Change the minimum value (for example "10") and click apply. Click an
arbitrary pixel within the brain. See how the brain is defined by red color

9) Keep changing the minimum value until you are satisfied with the way the
brain is defined by the red color.

10) Once you are satisfied, look at the "ROI Object" section and make sure
that "Object 1" is there. If not, right click the mouse buttons within the
square space below "ROI Objects" and define a new object

11) Click the "add" button in the "Selection" section. The red selected area
disappeared and defined by the "Object 1" color now.

12) Click the "+-/x" button in the "ROI" section. Choose the FA map in the
left and Object 1 in the right. In the middle box, choose "masking" and
click "OK". You should get a skull-stripped FA map.

------ Define the white matter ---------

13) Right click on the "Object 1" in the "ROI Objects" section and choose
"delete object".

14) Right click the empty square below the "ROI Objects" and choose "new
object". You redefined Object 1.

15) Choose the skull-stripped FA as the active image.

16) Choose "Seeded Region Growing". Choose "Absolute" and "3D" radio
buttons. Input 0.2 for the minimum and 1.0 for the maximum. Click on an
arbitrary pixel within the bright white matter area.

17) Click "Add" button. The red area turns into Object 1. If you find junk
pixels outside the white matter and want to manually touch up the result,
choose the "pencil" in the "Selection" section, write on the junk pixels
(red color appears), and click "Subtract" button.

18) Click the "save" icon in the "ROI" section. You can save the Object 1
that defines the white matter as Analyze or Binary.

Let me know if you are stuck or this doesn't work.

  _____  

From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of jiangxi
Sent: Friday, March 06, 2009 1:20 AM
To: mristudio-users at mristudio.org
Subject: Re: [Mristudio-users] Mean_ADC units

Hi,susumu
    Thanks for your advice. When I use the "thresholding" tool to define WM
cortex boundary with ranging from 0.15-0.25, it appears many red points in
the FA map to express the WM cortex. But I'm still confused with the
sequence steps: 1.How to save the red point- labeled FA map? 2.how can I use
the map to reconstruct the WM surface? 3.How can the reconstructed the WM
surface be visualized?   Many thanks!

  _____  

Date: Thu, 5 Mar 2009 14:28:52 -0500
From: susumu at mri.jhu.edu
To: mristudio-users at mristudio.org
Subject: Re: [Mristudio-users] Mean_ADC units

I suggest to use RoiEditor. Load your FA map and use the "thresholding" or
"region growing" tool to define the white matter - cortex boundary with FA =
0.15-0.25. This usually gives the good white matter surface.

If you need skullstip, load b0 or mean(DWI) image (you can create it by
DtiStudio) and use the thresholding or region growing tool to define the
brain outline. Register it as one object and use "+-/x" button to use the
object as "masking". This usually can clean up all the extra-cranial junks.

  _____  

From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of jiangxi
Sent: Wednesday, March 04, 2009 11:21 PM
To: mristudio-users at mristudio.org
Subject: Re: [Mristudio-users] Mean_ADC units

Hi,
  I'am wondering that how to use DTI data to reconstruct the cerebral cortex
surface or WM surface. The DTIStudio seems that can only carriy out to the
fiber-tracking step. Thanks!

> Date: Wed, 4 Mar 2009 15:55:29 -0500
> From: hjiang at jhmi.edu
> To: mristudio-users at mristudio.org
> Subject: Re: [Mristudio-users] Mean_ADC units
> 
> its unit is (mm^2/s) when you consider the b-value during the calculation.
> 
> hangyi
> 
> 
> 
> >>> Moran Artzi <artzimy at gmail.com> 03/04/09 2:34 PM >>>
> Hi
> what units are used when reporting the ADC Map - Mean value on the
> DTI-Studio Fiber Statistic option?
> ADC Map - Mean
> Max. of ImgVal: 4.2198
> Min. of ImgVal: 0.1643
> Mean of ImgVal: 0.9090
> Std. of ImgVal: 0.3467
> 
> Many thanks
> 
> Moran
> 
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> Mristudio-users mailing list
> Mristudio-users at mristudio.org
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