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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'>Hi Arun,<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'>It is likely that the difference is just 0
padding at the 182th, 218th, and 182th line. You can convert our 181x217x181
atlas to 182x218x182 using the "Crop" function in Landmarker. Another
possibility is that it was interpolated, which can also be done by Landmarker. You
may want to make sure by subtracting the images (you can do it in RoiEditor). <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'>We also got ICBM-152 from UCLA and don't
know why there are two versions with different dimensions. <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'>Susumu<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>
<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 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>Arun Bokde, PhD<br>
<b><span style='font-weight:bold'>Sent:</span></b> Tuesday, April 28, 2009 6:49
AM<br>
<b><span style='font-weight:bold'>To:</span></b> DTI Studio, ROI Editor,
Landmarker Questions/Support<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Mristudio-users]
human brain atlas</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 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;font-family:Calibri;color:#1F497D'>Hello,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;font-family:Calibri;color:#1F497D'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;font-family:Calibri;color:#1F497D'>The ICBM-152 Atlas
that comes from the UCLA web site has dimensions of 182 x 218 x 182 .
Within DTI Studio it is 181 x 217 x 181. There seems to be a single slice
difference between both templates? Where would the single slice
need to be added for both templates to match?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;font-family:Calibri;color:#1F497D'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;font-family:Calibri;color:#1F497D'>Regards,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;font-family:Calibri;color:#1F497D'>Arun<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;font-family:Calibri;color:#1F497D'><o:p> </o:p></span></font></p>
<div>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<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>susumu<br>
<b><span style='font-weight:bold'>Sent:</span></b> 26 January 2009 17:50<br>
<b><span style='font-weight:bold'>To:</span></b> 'DTI Studio, ROI Editor,
Landmarker Questions/Support'<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Mristudio-users]
human brain atlas<o:p></o:p></span></font></p>
</div>
</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 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>1) Landmarker can normalize your data to
ICBM-152. It comes with the ICBM (including our ICBM-DTI contrasts) and you can
doa linear or non-linear method.</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=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>2) If you already normalized to the
ICBM-152, the first step can be skipped. Just make sure the following;</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=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>> our ICBM-152 has 181x217x181 matrix
with 1 mm resolution</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=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>> You can load our ICBM-152 and your
normalized images to Landmarker (or any other software) to make sure that the
compatibility of two ICBM-152 (one you used and the other one implemented in
Landmarker and RoiEditor).</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=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>> Also, all of our software follows the
Radiology convention (right is left). If you find your image is loaded upside
down, that is because of the brain orientation issue. It is a good practice to
make sure right-left is correct in your entire procedure using a subject with
some characteristic asymmetry</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=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>3) Once you confirm that your ICBM atlas
was compatible with the one implemented in our software, do the following;</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=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>> Load your normalized data. If you
have lesion volume data (I assume it is 1/0 binary data), load it with some
anatomical image such as T2.</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=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>> Make sure that the image dimension is
181x217x181 / 1mm</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=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>> Then, choose "ICBM" as an
atlas in the right column</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=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>> There is a button looks like the
lung. Click it. This automatically segment your data into many white matter and
gray matter regions and give you a report. For your lesion image, you can get
how many "1 = lesion pixel" are in each segmented white matter area.</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=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>> If you want to see the segmentation
visually, use the "load" button in the "atlas" section and
load one of the "WMPM". You can visually see the superimiposition of
the segmentation on the loaded images.</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 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=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>Try</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 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'><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>
</span></font></div>
<p class=MsoNormal style='margin-bottom:12.0pt'><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>WangPing<br>
<b><span style='font-weight:bold'>Sent:</span></b> Monday, January 26, 2009
11:32 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]
human brain atlas<br>
<b><span style='font-weight:bold'>Importance:</span></b> High</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'>Susumu,<br>
<br>
I just played with RoiEditor for a while, and found the atlas with the
software. I am wondering if the tool (or you may recommend other tool)
can use the atlas to label my subjects. Right now my subjects have been
normalized to MNI152 space (non-linear registration), there are white matter
lesions on some subjects, I want to calculate the lesion volume on the white
matter regions. IF I can label my subjects, I will know the lesion volume
on each parcellation. I do not have to need a very detailed label atlas at this
point, maybe a atlas that can divide a brain into a few parcellations will be
okay.<br>
Thanks, any suggestion is high appreciated.<br>
Best Regards,<br>
<st1:place w:st="on">Ping</st1:place><br>
<br>
Date: Sun, 25 Jan 2009 08:38:18 -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] human brain atlas<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'>Hi Ping,</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 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'>We have several white matter atlases in
lbam.med.jhmi.edu, but the easiest way is to download Landmarker/RoiEditor from
<a href="http://www.mristudio.org/">www.mristudio.org</a>, which come with different
types of electronic atlases. One of them is population-averaged atlas in the
MNI coordinates. If you use linear normalization, I recommend using this atlas
(named ICBM_DTI-81 for GE/Siemens and JHU-MNI-GA for Philips). If you use
highly non-linear normalization, I recommend the single-subject atlas (named
JHU-MNI-SS). Both atlases come with a hand-segmented white matter parcellation
map (WMPM). If you download RoiEditor, this software can apply the WMPM for
various types of image quantification. Please refer to <a
href="http://www.mristudio.org/">www.mristudio.org</a> for more info.</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 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'>Susumu</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 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>WangPing<br>
<b><span style='font-weight:bold'>Sent:</span></b> Saturday, January 24, 2009
11:53 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> [Mristudio-users] human
brain atlas<br>
<b><span style='font-weight:bold'>Importance:</span></b> High</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=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'>Dear Dr. Mori and the List:<br>
<br>
Could anyone recommend a brain atlas (label atlas) that covers the
main white matters? It will be great if this atlas is easy to
register to MNI template.<br>
<br>
Thanks a lot!<br>
<st1:place w:st="on">Ping</st1:place><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>
</span></font></div>
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10.0pt'>立刻下载</span></font><font size=2 face=Verdana><span style='font-size:
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style='font-family:SimSun'>现在就下载！</span></font></a><o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=2 face=Verdana><span style='font-size:10.0pt;
font-family:Verdana'><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>
</span></font></div>
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10.0pt'>更多热辣资讯尽在新版</span></font><font size=2 face=Verdana><span
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