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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>OK, here is the procedure;<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>1) Please prepare one FA map and one b0
(or meanDWI)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>2) Load the FA map to RoiEditor using the
left upper "open" icon<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>3) Load the b0 (or meanDWI) using the
"open" icon in the right column, "Image" section.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>4) Make sure that you have FA and b0 both
loaded into one window using the pull-down menu in the "image"
section<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>------ Skull-stripping Using b0 (or
meanDWI) --------<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>5) Choose the b0 image as the active
image.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>6) Choose the "Seeded Region
Growing" tool in the "Tool" section<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>7) Choose "absolute" and
"3D" radio buttons.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>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<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>9) Keep changing the minimum value until
you are satisfied with the way the brain is defined by the red color.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>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<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>11) Click the "add" button in
the "Selection" section. The red selected area disappeared and
defined by the "Object 1" color now.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>------ Define the white matter ---------<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>13) Right click on the "Object
1" in the "ROI Objects" section and choose "delete
object".<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>14) Right click the empty square below the
"ROI Objects" and choose "new object". You redefined Object
1.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>15) Choose the skull-stripped FA as the
active image.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>18) Click the "save" icon in the
"ROI" section. You can save the Object 1 that defines the white
matter as Analyze or Binary.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Let me know if you are stuck or this
doesn't work.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<div>
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face=SimSun><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
mristudio-users-bounces@mristudio.org
[mailto:mristudio-users-bounces@mristudio.org] <b><span style='font-weight:
bold'>On Behalf Of </span></b><st1:State w:st="on"><st1:place w:st="on">jiangxi</st1:place></st1:State><br>
<b><span style='font-weight:bold'>Sent:</span></b> Friday, March 06, 2009 1:20 AM<br>
<b><span style='font-weight:bold'>To:</span></b> mristudio-users@mristudio.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Mristudio-users]
Mean_ADC units</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face=SimSun><span style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'>Hi,susumu<br>
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!<br>
<o:p></o:p></span></font></p>
<div class=MsoNormal align=center style='text-align:center'><font size=2
face=Verdana><span style='font-size:10.0pt;font-family:Verdana'>
<hr size=2 width="100%" align=center id=stopSpelling>
</span></font></div>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana'>Date: Thu, 5 Mar 2009 14:28:52
-0500<br>
From: <st1:PersonName w:st="on">susumu@mri.jhu.edu</st1:PersonName><br>
To: mristudio-users@mristudio.org<br>
Subject: Re: [Mristudio-users] Mean_ADC units<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>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.</span></font><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font><font size=2
face=Verdana><span style='font-size:10.0pt;font-family:Verdana'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>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.</span></font><font size=2
face=Verdana><span style='font-size:10.0pt;font-family:Verdana'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font><font size=2
face=Verdana><span style='font-size:10.0pt;font-family:Verdana'><o:p></o:p></span></font></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face=SimSun><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
mristudio-users-bounces@mristudio.org
[mailto:mristudio-users-bounces@mristudio.org] <b><span style='font-weight:
bold'>On Behalf Of </span></b><st1:State w:st="on"><st1:place w:st="on">jiangxi</st1:place></st1:State><br>
<b><span style='font-weight:bold'>Sent:</span></b> Wednesday, March 04, 2009
11:21 PM<br>
<b><span style='font-weight:bold'>To:</span></b> mristudio-users@mristudio.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Mristudio-users]
Mean_ADC units</span></font><font size=2 face=Verdana><span style='font-size:
10.0pt;font-family:Verdana'><o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 face=SimSun><span style='font-size:12.0pt'> </span></font><font
size=2 face=Verdana><span style='font-size:10.0pt;font-family:Verdana'><o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=2 face=Verdana><span
style='font-size:10.0pt;font-family:Verdana'>Hi,<br>
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!<br>
<br>
> Date: Wed, 4 Mar 2009 15:55:29 -0500<br>
> From: hjiang@jhmi.edu<br>
> To: mristudio-users@mristudio.org<br>
> Subject: Re: [Mristudio-users] Mean_ADC units<br>
> <br>
> its unit is (mm^2/s) when you consider the b-value during the calculation.<br>
> <br>
> hangyi<br>
> <br>
> <br>
> <br>
> >>> Moran Artzi <artzimy@gmail.com> 03/04/09 2:34 PM >>><br>
> Hi<br>
> what units are used when reporting the ADC Map - Mean value on the<br>
> DTI-Studio Fiber Statistic option?<br>
> ADC Map - Mean<br>
> Max. of ImgVal: 4.2198<br>
> Min. of ImgVal: 0.1643<br>
> Mean of ImgVal: 0.9090<br>
> Std. of ImgVal: 0.3467<br>
> <br>
> Many thanks<br>
> <br>
> Moran<br>
> <br>
> _______________________________________________<br>
> Mristudio-users mailing list<br>
> Mristudio-users@mristudio.org<br>
> http://lists.mristudio.org/mailman/listinfo/mristudio-users<o:p></o:p></span></font></p>
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