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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hello,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
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></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Regards,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Arun<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
mristudio-users-bounces@mristudio.org
[mailto:mristudio-users-bounces@mristudio.org] <b>On Behalf Of </b>susumu<br>
<b>Sent:</b> 26 January 2009 17:50<br>
<b>To:</b> 'DTI Studio, ROI Editor, Landmarker Questions/Support'<br>
<b>Subject:</b> Re: [Mristudio-users] human brain atlas<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
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><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:blue'>2) If you already normalized to the ICBM-152, the first step can be
skipped. Just make sure the following;</span><span style='font-size:10.0pt;
font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:blue'>> our ICBM-152 has 181x217x181 matrix with 1 mm resolution</span><span
style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
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><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
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><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:blue'>3) Once you confirm that your ICBM atlas was compatible with the
one implemented in our software, do the following;</span><span
style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
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><span
style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:blue'>> Make sure that the image dimension is 181x217x181 / 1mm</span><span
style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:blue'>> Then, choose "ICBM" as an atlas in the right column</span><span
style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
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><span
style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
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><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'> <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:blue'>Try</span><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p> </o:p></span></p>
<div class=MsoNormal align=center style='text-align:center'><span
style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>
<hr size=2 width="100%" align=center>
</span></div>
<p class=MsoNormal style='margin-bottom:12.0pt'><b><span style='font-size:10.0pt;
font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;
font-family:"Tahoma","sans-serif"'> mristudio-users-bounces@mristudio.org
[mailto:mristudio-users-bounces@mristudio.org] <b>On Behalf Of </b>WangPing<br>
<b>Sent:</b> Monday, January 26, 2009 11:32 AM<br>
<b>To:</b> mristudio-users@mristudio.org<br>
<b>Subject:</b> Re: [Mristudio-users] human brain atlas<br>
<b>Importance:</b> High</span><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:10.0pt;
font-family:"Verdana","sans-serif"'>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>
Ping<br>
<br>
Date: Sun, 25 Jan 2009 08:38:18 -0500<br>
From: susumu@mri.jhu.edu<br>
To: mristudio-users@mristudio.org<br>
Subject: Re: [Mristudio-users] human brain atlas<o:p></o:p></span></p>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:navy'>Hi Ping,</span><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'> <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
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><span
style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'> <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:navy'>Susumu</span><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'> <o:p></o:p></span></p>
<div>
<div class=MsoNormal align=center style='text-align:center'>
<hr size=2 width="100%" align=center>
</div>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
mristudio-users-bounces@mristudio.org [mailto:mristudio-users-bounces@mristudio.org]
<b>On Behalf Of </b>WangPing<br>
<b>Sent:</b> Saturday, January 24, 2009 11:53 PM<br>
<b>To:</b> mristudio-users@mristudio.org<br>
<b>Subject:</b> [Mristudio-users] human brain atlas<br>
<b>Importance:</b> High</span><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p></o:p></span></p>
</div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:10.0pt;
font-family:"Verdana","sans-serif"'>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>
Ping<br>
<br>
<o:p></o:p></span></p>
<div class=MsoNormal align=center style='text-align:center'><span
style='font-size:10.0pt;font-family:"Verdana","sans-serif"'>
<hr size=2 width="100%" align=center>
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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Verdana","sans-serif"'><o:p> </o:p></span></p>
<div class=MsoNormal align=center style='text-align:center'><span
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