Hi Chunxiao and Alex,<div><br></div><div>I would be cautious about using the gradient information in PAR file if you are using oblique-angle imaging.</div><div>For example, suppose you apply [1, 0, 0] gradient, which is along X (right - left). If you rotate the FOV about the Z axes, there are two ways to deliver [1, 0, 0]. In the first option, regardless of the rotation angle, the [1, 0, 0] is always the physical gradient X. In the second option, [1, 0, 0] rotates with FOV such that [1, 0, 0] gradient is always along the X axis of the image, meaning the combination of physical X and Y gradients (e.g. [0.9, 0.4, 0]).</div>
<div><br></div><div>Unless you are using "Overplus = on", the gradient table is automatically rotated to make sure [1, 0, 0] always means the X axis of the image, not the physical gradient. In this case, if the first line of the "vendor-supplied" table is [1, 0, 0], you can use the information as is. The problem is, if you read the gradient table from PAR file, I am not sure if it is stored in the image axes ([1, 0, 0]) or physical axes ([0.9, 0.4. 0]). If the latter is the case, you can't use the information as is.</div>
<div><br></div><div>I wonder if Jonathan or Bennett know the detail of the PAR file gradient table.</div><div><br></div><div>Susumu<br><br><div class="gmail_quote">On Thu, Dec 2, 2010 at 12:54 PM, Dresner, Alex <span dir="ltr"><<a href="mailto:alex.dresner@philips.com">alex.dresner@philips.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div lang="EN-US" link="blue" vlink="purple">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">Dear Andrew,
</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">Dr. Mori’s message was more complete than mine was, so I’ve copied his response below. In your .par file, you are correct that those three columns are your
diffusion directions. And though it says there are 33 directions, the last direction is 0.00, 0.00, 0.00 for the calculated DWI which should be replaced with 100, 100, 100 in your table for DTI Studio. And the direction before that (next-to-last in the .par
file) is the b0 image, because it is labeled with direction 0.00, 0.00, 0.00 and b-value = 1 (the column to the left of the gradient number, so those lines read … 1 33 0 0 0.000 0.000 0.000 …).</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">As far as checking the results to see if you have entered the correct gradient table, there’s no specific method. The easiest thing to do is to compare the
FA color map to that of the sample dataset and check obvious structures like the corpus callosum (should be red) and the optical fibers (should be green). Again I will quote Professor Mori: (DTI Studio mailing list, 6/10/10)</span></p>
<p class="MsoNormal" style="margin-left:.5in">There are several ways to notice wrong gradient tables;<br>
<br>
1) Totally wrong table: If the table is totally wrong, the color map doesn't make sense. So check color map first.<br>
2) X/Y/Z permutation: If X/Y/Z is miss signed, the color of the color maps doesn't look right. For example, the corpus callosum should look red, not green<br>
3) +/- sign error: Perform tractography. If sign is wrong, it doesn't make any sense.<br>
4) More subtle errors: Look at fitting residual (error) map. There is a file called "DtiStudioUpdate.doc" at
<a href="https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2" target="_blank">https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2</a>. This explains how to get the fitting error maps.<br>
5) Oblique angle: The attached file explains in detail. To make sure everything is right, you can scan a person twice. One in a regular position and one in severe oblique. If everything is working, you should get anatomically comparable tractography results.<br>
<br>
<span style="font-size:11.0pt;color:#1F497D"></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">Regards,</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">Alex</span></p><div class="im">
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"> </span></p>
<p class="MsoNormal">Dear Alex,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Thank you very much for your prompt response.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"> The attached is my .par file. Do you mean that the "# diffusion (ap, fh, rl) (3*float)" , for example -0.001 -0.076 -0.997, is a diffusion direction? Since there are 33 directions in my .PAR file and are labeled from 1 to 33,
should I change their label to 0,1,..32? In addition , should I add a extra line (33) with 100, 100, 100 in the end of the gradient table?</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">By the way, is there any way based on the result I can check whether I use the right gradient table?</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Again, thank you for your time and help!</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal" style="margin-bottom:12.0pt">Chunxiao(Andrew)</p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;color:#1F497D"> </span></b></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"> </span></p>
</div><div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:10.0pt">From:</span></b><span style="font-size:10.0pt"> <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>On Behalf Of </b>susumu mori<br>
<b>Sent:</b> Wednesday, November 24, 2010 6:27 AM<br>
<b>To:</b> DTI Studio, ROI Editor, DiffeoMap Questions/Support<br>
<b>Subject:</b> Re: [Mristudio-users] Gradient Table for Philips</span></p>
</div>
<p class="MsoNormal"> </p>
<p class="MsoNormal">1) Please read your REC file using Mri3DView. Use the image dimensions you get from the PAR file.</p>
<div>
<p class="MsoNormal">2) After the images are read, please go through the images using the pull-down menu in the right column of the viewing window. Check if all the images (b0 and DWIs) look fine.</p>
</div>
<div>
<p class="MsoNormal">3) Find out how many 3D images are loaded. If you used Philips "High" gradient orientation, you should have 34 images loaded; one b0, 32 DWIs, and one calculated DWIs (I think this is the sum of all DWIs).</p>
</div>
<div>
<p class="MsoNormal">4) Make sure where is b0. It could be the first or the second from the last. The calculated DWI is always at the end.</p>
</div>
<div>
<p class="MsoNormal">5) Close the window and start DtiMapping.</p>
</div>
<div>
<p class="MsoNormal">6) Cut&Paste your gradient table to the appropriate section. You have to make sure several things here;</p>
</div>
<div>
<p class="MsoNormal">a: The position of b0; First or the second from the last</p>
</div>
<div>
<p class="MsoNormal">b: The number of rows; It has to be 34. Sometimes you find a table with only 33 lines ignoring the last calculated image. In this case, you get the error message, complaining that the file size doesn't match. Because the last image is not
used anyway, you can ignore the message and proceed. The last image is thrown away. Or, you can increase the number of row to 34 by adding 33: 100, 100, 100, in which [100, 100, 100] send the message to DtiStudio to remove this image.</p>
</div>
<div>
<p class="MsoNormal">c: Please make sure if you used "gradient overplus ON" or "OFF", because you have to use different tables.</p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt">7) If you still get the file size error message, something is wrong.</p>
<div><div class="im">
<p class="MsoNormal">On Tue, Nov 23, 2010 at 5:21 PM, Dresner, Alex <<a href="mailto:alex.dresner@philips.com" target="_blank">alex.dresner@philips.com</a>> wrote:</p>
</div><div>
<div><div class="im">
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">Dear Chunxiao,
</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">Your gradient table is also in the .PAR file. You should be able to read the .PAR file with any text reader such as WordPad, NotePad
or Word; lower in the file is a table of parameters per-image. On the right-hand-side of that table are the diffusion directions in three columns.</span><span style="color:#1F497D"></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">Regards,</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">Alex</span><span style="color:#1F497D"></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">____________________</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">M. Alex Dresner, Ph.D.</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">MR Clinical Scientist</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"><a href="mailto:alex.dresner@philips.com" target="_blank">alex.dresner@philips.com</a></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">____________________</span><span style="color:#1F497D"></span></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:10.0pt">From:</span></b><span style="font-size:10.0pt">
<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>On Behalf Of </b>Chunxiao Zhou<br>
<b>Sent:</b> Tuesday, November 23, 2010 5:07 PM<br>
<b>To:</b> <a href="mailto:mristudio-users@mristudio.org" target="_blank">mristudio-users@mristudio.org</a><br>
<b>Subject:</b> [Mristudio-users] Gradient Table for Philips</span></p>
</div>
</div><div>
<div><div class="im">
<p class="MsoNormal"> </p>
<div>
<p class="MsoNormal">Hello,<span style="color:#1F497D"></span></p>
</div>
<div>
<p class="MsoNormal">When I do tensor calculation for my own data , there is a warning message "File size is bigger than DW-image size, continue anyway?". I get all image size parameters from my .par
file ( I use Philip .REC .PAR data). I guess the reason is that I use the default
<span lang="EN">ParRec gradient table from your GradientTable file. How could I get my gradient table from my file?
</span><span style="color:#1F497D"></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN">Thank you.</span><span style="color:#1F497D"></span></p>
</div>
</div><div>
<p class="MsoNormal"><span lang="EN">Chunxiao(Andrew)</span></p><div class="im"><br>
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