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Susumu, thank you very much. Ping<br><br><hr id="stopSpelling">Date: Mon, 26 Jan 2009 12:50:23 -0500<br>From: susumu@mri.jhu.edu<br>To: mristudio-users@mristudio.org<br>Subject: Re: [Mristudio-users] human brain atlas<br><br>
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<div dir="ltr" align="left"><span class="EC_699013717-26012009"><font color="#0000ff" face="Arial">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.</font></span></div>
<div dir="ltr" align="left"><span class="EC_699013717-26012009"><font color="#0000ff" face="Arial">2) If you already normalized to the ICBM-152, the first step can
be skipped. Just make sure the following;</font></span></div>
<div dir="ltr" align="left"><span class="EC_699013717-26012009"><font color="#0000ff" face="Arial">> our ICBM-152 has 181x217x181 matrix with 1 mm
resolution</font></span></div>
<div dir="ltr" align="left"><span class="EC_699013717-26012009"><font color="#0000ff" face="Arial">> 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).</font></span></div>
<div dir="ltr" align="left"><span class="EC_699013717-26012009"><font color="#0000ff" face="Arial">> 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</font></span></div>
<div dir="ltr" align="left"><span class="EC_699013717-26012009"><font color="#0000ff" face="Arial">3) Once you confirm that your ICBM atlas was compatible with the
one implemented in our software, do the following;</font></span></div>
<div dir="ltr" align="left"><span class="EC_699013717-26012009"><font color="#0000ff" face="Arial">> 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.</font></span></div>
<div dir="ltr" align="left"><span class="EC_699013717-26012009"><font color="#0000ff" face="Arial">> Make sure that the image dimension is 181x217x181 /
1mm</font></span></div>
<div dir="ltr" align="left"><span class="EC_699013717-26012009"><font color="#0000ff" face="Arial">> Then, choose "ICBM" as an atlas in the right
column</font></span></div>
<div dir="ltr" align="left"><span class="EC_699013717-26012009"><font color="#0000ff" face="Arial">> 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.</font></span></div>
<div dir="ltr" align="left"><span class="EC_699013717-26012009"><font color="#0000ff" face="Arial">> 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.</font></span></div>
<div dir="ltr" align="left"><span class="EC_699013717-26012009"><font color="#0000ff" face="Arial"></font></span> </div>
<div dir="ltr" align="left"><span class="EC_699013717-26012009"><font color="#0000ff" face="Arial">Try</font></span></div><br>
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<font face="Tahoma"><b>From:</b> 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<br></font><br></div>
<div></div>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<br><br>
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<p class="EC_EC_MsoNormal"><font color="navy" face="Arial"><span style="font-size: 10pt; color: navy; font-family: Arial;">Hi
Ping,</span></font></p>
<p class="EC_EC_MsoNormal"><font color="navy" face="Arial"><span style="font-size: 10pt; color: navy; font-family: Arial;"></span></font> </p>
<p class="EC_EC_MsoNormal"><font color="navy" face="Arial"><span style="font-size: 10pt; color: navy; font-family: Arial;">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></p>
<p class="EC_EC_MsoNormal"><font color="navy" face="Arial"><span style="font-size: 10pt; color: navy; font-family: Arial;"></span></font> </p>
<p class="EC_EC_MsoNormal"><font color="navy" face="Arial"><span style="font-size: 10pt; color: navy; font-family: Arial;">Susumu</span></font></p>
<p class="EC_EC_MsoNormal"><font color="navy" face="Arial"><span style="font-size: 10pt; color: navy; font-family: Arial;"></span></font> </p>
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<p class="EC_EC_MsoNormal"><b><font face="Tahoma" size="2"><span style="font-weight: bold; font-size: 10pt; font-family: Tahoma;">From:</span></font></b><font face="Tahoma" size="2"><span style="font-size: 10pt; 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></p></div>
<p class="EC_EC_MsoNormal"><font face="SimSun" size="3"><span style="font-size: 12pt;"></span></font> </p>
<p class="EC_EC_MsoNormal" style="margin-bottom: 12pt;"><font face="Verdana" size="2"><span style="font-size: 10pt; 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>Ping<br><br><br></span></font></p>
<div class="EC_EC_MsoNormal" style="text-align: center;" align="center"><font face="Verdana" size="2"><span style="font-size: 10pt; font-family: Verdana;">
<hr align="center" size="2" width="100%">
</span></font></div>
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