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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">Joe, unfortunately this is a variable.</span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span style="font-size:
10.0pt;font-family:Arial;color:navy">Depends on the release. The table has changed over the years.</span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span style="font-size:
10.0pt;font-family:Arial;color:navy">Do you know the release?</span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span style="font-size:
10.0pt;font-family:Arial;color:navy">The directions can also be obtained from the DICOM files if you have them.</span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span style="font-size:
10.0pt;font-family:Arial;color:navy">-roddy</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></p>
<div>
<div class="MsoNormal" align="center" style="text-align:center"><font size="3" face="Times New Roman"><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>Wu, Joseph<br>
<b><span style="font-weight:bold">Sent:</span></b> Friday, October 22, 2010 12:15 PM<br>
<b><span style="font-weight:bold">To:</span></b> DTI Studio, ROI Editor, DiffeoMap Questions/Support<br>
<b><span style="font-weight:bold">Subject:</span></b> [Mristudio-users] Need GE 3 tesla 25 direction DTI gradient table please, thanks</span></font></p>
</div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"> </span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:Calibri;color:#1F497D">Hi
</span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:Calibri;color:#1F497D">Does somebody have GE 3 tesla 25 direction DTI gradient table that they can forward to :
<a href="mailto:jcwu@uci.edu">jcwu@uci.edu</a>? That would be greatly appreciated.
</span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:Calibri;color:#1F497D">Thanks,</span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:Calibri;color:#1F497D">Joe</span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:Calibri;color:#1F497D"> </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>Xu Li<br>
<b><span style="font-weight:bold">Sent:</span></b> Thursday, October 21, 2010 8:18 AM<br>
<b><span style="font-weight:bold">To:</span></b> DTI Studio, ROI Editor, DiffeoMap Questions/Support<br>
<b><span style="font-weight:bold">Subject:</span></b> Re: [Mristudio-users] problems with gradients</span></font></p>
</div>
</div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"> </span></font></p>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">Dear Susumu,</span></font></p>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">I have a quick question about the gradient table I got from the gradient_table_creator</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">It gives me a table with the [0 0 0] and [100 100 100] at the bottom which seems to be different than those sample gradient table I have from DTI_studio. Should I just
move the [0 0 0] to the top? Or the 3T Philips systems do the b0 scan at the end instead of at the beginning now?</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"> </span></font></p>
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<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">Thanks!</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">Xu</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"> </span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"> </span></font></p>
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<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">On Oct 20, 2010, at 10:19 PM, susumu mori wrote:</span></font></p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">Hi Jill,</span></font></p>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">I'm second to SC. When you are using Philips, even if you thought that you are using exactly the same parameters, you could end up in two different types of the gradient
tables; overplus on and off. This is not recorded in the beginning of PAR file.</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">So my suggestion is, try the "overplus on" option of the table calculator.</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">Also, if you find that you used "overplus on", you have to type in the oblique angle information in the calculator. The angle information is in the PAR file.</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">The reason you didn't get the tractography right is most likely due to "+/-" signs of the gradient table you used. You can test "x/y/z flip" function of the tractography
to test it. The best way is to use the gradient calculator, which should be able to sort out all the issues.</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">Susumu</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"> </span></font></p>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">On Tue, Oct 19, 2010 at 4:52 PM, Zwicker, Jill <<a href="mailto:JZwicker@cw.bc.ca">JZwicker@cw.bc.ca</a>> wrote:</span></font></p>
<div>
<div>
<p class="MsoNormal"><font size="2" color="black" face="Tahoma"><span style="font-size:
10.0pt;font-family:Tahoma;color:black">Further to this message, the ROI values I get are consistent with the previous scans, so it is just the fiber tracking that I am
suspicious of...</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="2" face="Tahoma"><span style="font-size:10.0pt;
font-family:Tahoma">Thanks!</span></font></p>
</div>
<div>
<div class="MsoNormal" align="center" style="text-align:center"><font size="3" face="Times New Roman"><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">
<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a> [<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>] On Behalf Of Zwicker, Jill [<a href="mailto:JZwicker@cw.bc.ca" target="_blank">JZwicker@cw.bc.ca</a>]<br>
<b><span style="font-weight:bold">Sent:</span></b> October 19, 2010 1:26 PM</span></font></p>
<div>
<p class="MsoNormal"><font size="2" face="Tahoma"><span style="font-size:10.0pt;
font-family:Tahoma"><br>
<b><span style="font-weight:bold">To:</span></b> DTI Studio, ROI Editor, DiffeoMap Questions/Support</span></font></p>
</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">Subject:</span></font></b><font size="2" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma"> Re:
[Mristudio-users] problems with gradients</span></font></p>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><font size="2" color="black" face="Tahoma"><span style="font-size:
10.0pt;font-family:Tahoma;color:black">Hi Susumu and SC,</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="2" face="Tahoma"><span style="font-size:10.0pt;
font-family:Tahoma">You previously helped me with a tensor calc issue (see below). I have since used the gradient calculator and obtained more RAM, and have successfully analyzed
two scans. However, the remaining scans are not processing properly (i.e., I do not get a proper colour map). In looking at the PAR files, the parameters are the same as the first two scans, with the exception of the rescale and scale slopes, window center
and widths, and diffision parameters (nothing that changes what I enter to the online gradient table calculator). Since the gradient table I was using didn't work for successive scans, I took the gradients from the PAR file. This seemed to work, but the colours
were reversed, so I switched coloumns around and got a seemingly accurate colour map. However, when I tried to fiber track, the CST seems too short and the values are not consistent with what I obtained in the previous 2 scans.</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="2" face="Tahoma"><span style="font-size:10.0pt;
font-family:Tahoma">So...I am unsure why the previous gradient table didn't work and I don't think my trial and error method of getting a colour map is accurate. I would be happy
to send you the PAR files (off the listserv) if that would help.</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="2" face="Tahoma"><span style="font-size:10.0pt;
font-family:Tahoma">Thank you in advance for your guidance.</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="2" face="Tahoma"><span style="font-size:10.0pt;
font-family:Tahoma">Jill</span></font></p>
</div>
<div>
<div class="MsoNormal" align="center" style="text-align:center"><font size="2" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma">
<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">
<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a> [<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>] On Behalf Of susumu mori [<a href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>]<br>
<b><span style="font-weight:bold">Sent:</span></b> September 1, 2010 6:25 PM<br>
<b><span style="font-weight:bold">To:</span></b> DTI Studio, ROI Editor, DiffeoMap Questions/Support<br>
<b><span style="font-weight:bold">Subject:</span></b> Re: [Mristudio-users] problems with tensor calc</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">I suspect memory problem.
</span></font></p>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">Please use stricter threshold (like FA>0.3 and angle <30, for example) to see if it works. If it works, then it's memory problem (I mean, you need more memory).</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">You can also save eigenvector0 and FA, close DtiStudio, and redo fiber tracking using the saved file. If you start from tensor calculation, you have all the raw data
in your memory.</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">32-bit operating system can allocate only 1-1.5GB memory. 64bit is much better.</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">susumu</span></font></p>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">On Wed, Sep 1, 2010 at 2:55 PM, Zwicker, Jill <<a href="mailto:JZwicker@cw.bc.ca" target="_blank">JZwicker@cw.bc.ca</a>> wrote:</span></font></p>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">Thank you so much! After some trial and error, I figured out the correct gradient table. I can now get a beautiful colour map, but I have a new problem. The program
crashes everytime I try to do fibre tracking. Any suggestions?</span></font></p>
<div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><br>
-----Original Message-----<br>
From: <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>] On Behalf Of [Seongjin]<br>
Sent: Wednesday, September 01, 2010 10:56 AM<br>
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support<br>
Subject: Re: [Mristudio-users] problems with tensor calc<br>
<br>
Use the following link for the gradient table calculation.<br>
You need to get some information required to fill in from Par file of your data.<br>
If your data is not in ParRec format, get it first.<br>
<br>
<a href="http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html" target="_blank">http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html</a><br>
<br>
-SC.<br>
<br>
On Wed, Sep 1, 2010 at 1:46 PM, Zwicker, Jill <<a href="mailto:JZwicker@cw.bc.ca" target="_blank">JZwicker@cw.bc.ca</a>> wrote:<br>
> Hi DTI Studio users,<br>
><br>
> I am relatively new to DTI studio and have been using successfully to do<br>
> tractography on infant brain data collected on a Seimens. I am now trying to<br>
> analyze child brain data collected on a Philips. I can get a clear image,<br>
> but as soon as I try a tensor calculation, the image quality degrades<br>
> significantly (no matter what the background noise level I set it to). I<br>
> made gradient tables from the PAR file (forwards and backwards) and also<br>
> flipped the z as the tutorial suggests. Any suggestions on how I can solve<br>
> this problem?<br>
><br>
> Thanks for your help.<br>
><br>
><br>
><br>
> Jill Zwicker, PhD, OT(C)<br>
><br>
> Postdoctoral Fellow<br>
><br>
> Child & Family Research Institute<br>
><br>
> Developmental Neurosciences & Child Health<br>
><br>
> L408 - 4480 Oak Street<br>
><br>
> Vancouver, BC V6H 3V4<br>
><br>
> Phone: 604-875-2000 ext 6805<br>
><br>
> Fax: 604-875-3569<br>
><br>
> <a href="mailto:jzwicker@cw.bc.ca" target="_blank">jzwicker@cw.bc.ca</a><br>
><br>
><br>
><br>
> _______________________________________________<br>
> mristudio-users mailing list<br>
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><br>
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