Thanks for your comment.<br><br>-SC<br><br><div class="gmail_quote">On Fri, May 8, 2009 at 10:54 AM, susumu <span dir="ltr"><<a href="mailto:susumu@mri.jhu.edu">susumu@mri.jhu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<p><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">Yes. That's the idea. </span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">One thing you have to be careful is, if
you have repeated dataset, like 3 sets of 12-orientation measurements.</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">After AIR, each DWI could be rotated in a different
way and therefore obtain a new gradient orientation.</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">That means, the 3 repeated measurements
may no longer have the same 12-orientation gradient table. Instead, you will
get 36 orientations. Therefore, you have to combine all 3 sets to create one
measurement with 36 orientations and your gradient table also has to be one
36-orientation table.</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">Is this correct, Hangyi?</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">In DtiStudio, you can create average and
subtracted images of repeated measurements using the "mean, STD"
button. From these images, you can get idea about how much translation and
rotation occurred during the scans. Usually, the rotation is very tiny, like
within 1 degree. In this case, you don't have to use gradient table rotation,
in my opinion. Unless you have a bad data in which subject was moving more than
few degrees, this rotation correction may not have much importance. On the
other hand, if the subject is moving around, you may have other issues like
image corruptions and motion within one image (odd and even slices are not
registered), which can not be solved by AIR.</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">So, I guess what I'm saying is you should
carefully inspect your data, instead of just throwing your data into AIR, do
gradient table rotation, and forget about it.</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
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<p><b><font size="2" face="Tahoma"><span style="font-size: 10pt; font-family: Tahoma; font-weight: bold;">From:</span></font></b><font size="2" face="Tahoma"><span style="font-size: 10pt; font-family: Tahoma;">
<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a> [mailto:<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>]
<b><span style="font-weight: bold;">On Behalf Of </span></b>[Seongjin]<br>
<b><span style="font-weight: bold;">Sent:</span></b> Thursday, April 30, 2009
3:32 PM<div class="im"><br>
<b><span style="font-weight: bold;">To:</span></b> DTI Studio, ROI Editor,
Landmarker Questions/Support<br>
</div><b><span style="font-weight: bold;">Subject:</span></b> Re: [Mristudio-users]
Gradient table</span></font></p>
</div><div><div></div><div class="h5">
<p><font size="3" face="Times New Roman"><span style="font-size: 12pt;"> </span></font></p>
<p style="margin-bottom: 12pt;"><font size="3" face="Times New Roman"><span style="font-size: 12pt;">After AIR registration
(with option modified gradient table if available...), I have a new gradient
table in AirMatrix.txt file.<br>
Then I loaded AIR registered image and the new gradient table for tensor
calculation and tractography. <br>
Am I doing right?<br>
Thanks in advance.<br>
<br>
-SC</span></font></p>
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<p><font size="3" face="Times New Roman"><span style="font-size: 12pt;">On Thu, Apr 30, 2009 at 1:18 PM, susumu <<a href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>> wrote:</span></font></p>
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<p><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">The gradient table for Philips scanner calculated by this
program is "correct", meaning no flipping and other modifications are
necessary.</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;">I strong encourage users to use this program if you are using
the "overplus" option + oblique slice. You can type in the oblique
angles and get a recalculated table.</span></font></p>
<p><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<div>
<div style="text-align: center;" align="center"><font size="3" face="Times New Roman"><span style="font-size: 12pt;">
<hr size="2" width="100%" align="center">
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<p><b><font size="2" face="Tahoma"><span style="font-size: 10pt; font-family: Tahoma; font-weight: bold;">From:</span></font></b><font size="2" face="Tahoma"><span style="font-size: 10pt; font-family: Tahoma;"> <a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>
[mailto:<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>]
<b><span style="font-weight: bold;">On Behalf Of </span></b>[Seongjin]<br>
<b><span style="font-weight: bold;">Sent:</span></b> Thursday, April 30, 2009
12:28 PM<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> [Mristudio-users]
Gradient table</span></font></p>
</div>
<div>
<div>
<p><font size="3" face="Times New Roman"><span style="font-size: 12pt;"> </span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size: 12pt;">I
appreciate the tutorial session at Queen's Medical
Center in Honolulu.<br>
<br>
I am using gradient table (for DTI studio ) generated at the following link:<br>
<a href="http://godzilla.kennedykrieger.org/%7Ejfarrell/OTHERphilips/GUI.html" target="_blank">http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html</a><br>
<br>
I wonder if I can directly use the gradient table from this java applet without
field flipping.<br>
Thanks in advance.<br>
<br>
-SC</span></font></p>
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