<div>Hi Hangji,</div>
<div> I figured out that it was Philips 3T scanner (but we still don't know what kind, though it is out of state scanner images we got), and it has 25 gradient directions (including the bo image). I used the following gradient table:</div>
<p style="LINE-HEIGHT:normal;MARGIN:0in 0in 0pt" class="MsoNormal"><span style><font size="3"><font face="Calibri">0: 0, 0, 0</font></font></span></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>1: </span>0.532212965784<span style>,</span> 0.104012540712<span style>,</span> -0.840196852187</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>2: </span>0.250139840140<span style>,</span> -0.721834058886<span style>,</span> 0.645279514479</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>3: </span>-0.633506688611<span style>,</span> -0.753135632571<span style>,</span> -0.177358378534</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>4: </span>-0.218922463231<span style>,</span> 0.850392517067<span style>,</span> 0.478440719431</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>5: </span>-0.413149806364<span style>,</span> -0.780294228218<span style>,</span> 0.469519067675</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>6: </span>0.734236034340<span style>,</span> -0.661803691272<span style>,</span> 0.151371463942</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>7: </span>0.936469940841<span style>,</span> 0.054189066241<span style>,</span> 0.346536570943</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>8: </span>-0.333112408327<span style>,</span> -0.242859001882<span style>,</span> 0.911073887576</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>9: </span>0.103315488089<span style>,</span> -0.991677012629<span style>,</span> -0.076828461807</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>10: </span>-0.926539655526<span style>,</span> 0.372983070696<span style>,</span> -0.049070313963</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>11: </span>0.801488967040<span style>,</span> 0.543143312217<span style>,</span> -0.250221458126</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>12: </span>-0.916836769339<span style>,</span> -0.261947685782<span style>,</span> 0.301320009791</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>13: </span>-0.537755795155<span style>,</span> 0.438027927278<span style>,</span> -0.720382009562</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>14: </span>-0.213559057919<span style>,</span> -0.664684481487<span style>,</span> -0.715951862105</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>15: </span>-0.124138610474<span style>,</span> -0.051815651202<span style>,</span> -0.990911067493</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>16: </span>0.273979937314<span style>,</span> 0.960273112918<span style>,</span> -0.053014550417</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>17: </span>-0.443315490443<span style>,</span> 0.878048334487<span style>,</span> -0.180284492503</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>18: </span>0.024170841904<span style>,</span> 0.368771526312<span style>,</span> 0.929205753202</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>19: </span>0.568365159741<span style>,</span> 0.637098308775<span style>,</span> 0.520640749604</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>20: </span>0.930930389545<span style>,</span> -0.168157726945<span style>,</span> -0.324178328533</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>21: </span>-0.825458835938<span style>,</span> -0.182178469442<span style>,</span> -0.534255290516</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>22: </span>0.472597880311<span style>,</span> -0.629557481175<span style>,</span> -0.616691674520</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>23: </span>0.504263360030<span style>,</span> -0.129264527496<span style>,</span> 0.853820323992</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>24: </span>0.149335563174<span style>,</span> 0.688742589708<span style>,</span> -0.709459325610</font></p>
<p style="MARGIN:0in 0in 0pt" class="MsoPlainText"><font face="Courier New"><span style>25: </span>-0.694717409994<span style>,</span> 0.344411933027<span style>,</span> 0.631465074759</font></p>
<div> But unfortunately, the image quality looks very bad for the color map images...</div>
<div>I'll appreciate your reply.</div>
<div> </div>
<div>Thanks</div>
<div>Supreet.<br><br></div>
<div class="gmail_quote">On Fri, Jan 27, 2012 at 2:22 PM, Hangyi Jiang <span dir="ltr"><<a href="mailto:hjiang@jhmi.edu">hjiang@jhmi.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">hi,Supreet<br><br> seems that your dataset has not being loaded in correctly, or they are not in Siemens Mosaic format.<br>
<br>you said that the dataset has " 25 gradient directions", right? if so, you will get 25 image volumes (and maybe more, since B0 images) after "File->Dti Mapping -> Siemens Mosaic...". please double check if the images are loaded in correctly before you figure out the gradient table.<br>
<br>regards,<br>
<div class="im"><br>hangyi<br><br><br><br><br><br>________________________________________<br>From: Supreet kaur [<a href="mailto:ksupreet6@gmail.com">ksupreet6@gmail.com</a>]<br></div>Sent: Friday, January 27, 2012 1:31 PM<br>
To: Hangyi Jiang<br>Subject: Re: DTI gradient table<br>
<div>
<div class="h5"><br>Hi Hangyi,<br> When I do the steps as you suggested , it gives a the following: I don't know what to do at this point, Please help<br><br>0: 0.000000, 0.000000, 0.000000, 1703965<br>
1: 0.000000, 0.000000, 0.000000, 524297<br>2: 0.000000, 0.000000, 0.000000, 1507345<br>3: 0.000000, 0.000000, 0.000000, 851980<br>4: 0, 0, 0, 0<br>5: 0, 0, 0, 0<br>6: 0, 0, 0, 0<br>7: 0, 0, 0, 0<br>8: 0, 0, 0, 0<br>9: 0, 0, 0, 0<br>
10: 0, 0, 0, 0<br>11: 0, 0, 0, 0<br>12: 0, 0, 0, 0<br>13: 0, 0, 0, 0<br>14: 0, 0, 0, 0<br>15: 0, 0, 0, 0<br>16: 0, 0, 0, 0<br>17: 0, 0, 0, 0<br>18: 0, 0, 0, 0<br>19: 0, 0, 0, 0<br>20: 0, 0, 0, 0<br>21: 0, 0, 0, 0<br>22: 0, 0, 0, 0<br>
23: 0, 0, 0, 0<br>24: 0, 0, 0, 0<br>25: 0, 0, 0, 0<br>26: 0, 0, 0, 0<br>27: 0, 0, 0, 0<br>28: 0, 0, 0, 0<br>29: 0, 0, 0, 0<br>30: 0, 0, 0, 0<br>31: 0, 0, 0, 0<br>32: 0, 0, 0, 0<br>33: 0, 0, 0, 0<br>34: 0, 0, 0, 0<br>35: 0, 0, 0, 0<br>
36: 0, 0, 0, 0<br>37: 0, 0, 0, 0<br>38: 0, 0, 0, 0<br>39: 0, 0, 0, 0<br>40: 0, 0, 0, 0<br>41: 0, 0, 0, 0<br>42: 0, 0, 0, 0<br>43: 0, 0, 0, 0<br>44: 0, 0, 0, 0<br>45: 0, 0, 0, 0<br>46: 0, 0, 0, 0<br>47: 0, 0, 0, 0<br>48: 0, 0, 0, 0<br>
49: 0, 0, 0, 0<br>50: 0, 0, 0, 0<br>51: 0, 0, 0, 0<br>52: 0, 0, 0, 0<br>53: 0, 0, 0, 0<br>54: 0, 0, 0, 0<br>55: 0, 0, 0, 0<br>56: 0, 0, 0, 0<br>57: 0, 0, 0, 0<br>58: 0, 0, 0, 0<br>59: 0, 0, 0, 0<br>60: 0, 0, 0, 0<br>61: 0, 0, 0, 0<br>
62: 0, 0, 0, 0<br>63: 0, 0, 0, 0<br><br></div></div>
<div class="im">On Fri, Jan 27, 2012 at 1:11 PM, Hangyi Jiang <<a href="mailto:hjiang@jhmi.edu">hjiang@jhmi.edu</a><mailto:<a href="mailto:hjiang@jhmi.edu">hjiang@jhmi.edu</a>>> wrote:<br><br>if the dataset is saved as Siemens Mosaic format, you can try to get the gradients from file header.<br>
try this: File->DtiMapping -> Siemens Mosaic ->.. specify the file name (actually folder name).. clicking "get gradients from file header" button....;<br><br>let me know if you have any problems..<br><br>
hangyi<br><br>hangyi<br><br><br><br><br><br><br>________________________________________<br></div>From: Supreet kaur [<a href="mailto:ksupreet6@gmail.com">ksupreet6@gmail.com</a><mailto:<a href="mailto:ksupreet6@gmail.com">ksupreet6@gmail.com</a>>]<br>
<div class="im">Sent: Friday, January 27, 2012 12:15 PM<br>To: DTI Studio, ROI Editor, DiffeoMap Questions/Support<br>Cc: Hangyi Jiang; Susumu Mori<br>Subject: DTI gradient table<br><br>Dear DTI experts,<br> I have a DTI data with 25 gradient directions, what gradient table should we use for that?<br>
Its a Siemens 3T scanner...<br>I'll appreciate your help.<br><br>Thanks<br><br>Sincerely,<br><br>Supreet kaur,<br>Biomedical research engineer,<br>Nationwide Childrens Hospital,<br>Columbus, OH<br></div><a href="tel:%28614%29355-3509" value="+16143553509">(614)355-3509</a><tel:%28614%29355-3509><br>
<div class="HOEnZb">
<div class="h5"><br><br><br><br>--<br>Sincerely,<br><br>Supreet kaur,<br>Biomedical research engineer,<br>Nationwide Childrens Hospital,<br>Columbus, OH<br><a href="tel:%28614%29355-3509" value="+16143553509">(614)355-3509</a><br>
<br></div></div></blockquote></div><br><br clear="all"><br>-- <br>
<div>Sincerely,<br><br>Supreet kaur,</div>
<div>Biomedical research engineer,<br>Nationwide Childrens Hospital,<br>Columbus, OH<br>(614)355-3509</div><br>