<div>Hello,</div>
<div> </div>
<div>Thanks for the reply. I am facing a problem regarding the reconstruction of fibre tracts. I want to track the CST fibres of a tumor patient, after placing the ROI on the CST at the level of medulla the tracts are generated but they are not exactly the same as shown in publications (reconstructed fibers are not fine and refined). </div>
<div> </div>
<div>I have taken the following fiber tracking parameters:</div>
<div> </div>
<div>Start Tracking</div>
<div>if FA>0.25</div>
<div> </div>
<div>Stop Tracking</div>
<div>if FA<0.25</div>
<div>if Tract turning-angle>45</div>
<div> </div>
<div>Flip Eigen Vector</div>
<div> </div>
<div>X, Y, Z components have been checked</div>
<div> </div>
<div>I am attaching a print screen shot of the image, please suggest some changes.<br></div>
<div>regards</div>
<div> </div>
<div>sona<br></div>
<div class="gmail_quote">On Mon, Jan 11, 2010 at 11:56 AM, susumu mori <span dir="ltr"><<a href="mailto:susumu@mri.jhu.edu">susumu@mri.jhu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">The statistics in the ROI panel is to measure pixel values inside the ROI. It is just a simple ROI-based quantification.<br>
<br>In the fiber panel, you draw ROI to create tract paths. Then the quantification is based on pixel values of the reconstructed fibers.
<div>
<div></div>
<div class="h5"><br><br>
<div class="gmail_quote">On Fri, Jan 8, 2010 at 3:47 PM, Sona Saksena <span dir="ltr"><<a href="mailto:saksena.sona@gmail.com" target="_blank">saksena.sona@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">
<div>Hello,</div>
<div> </div>
<div>After placing the ROI, the statistics for the mostly recent ROI is shown in the fiber control panel. What is the difference between the statistics after pressing the "Go button" in the "Fiber Statistics" option and the most recent statisitcs in the ROI control panel. What should I take for my final calculations and results.</div>
<div> </div>
<div>Please do suggest.</div>
<div> </div>
<div>thanks</div>
<div> </div>
<div>regards</div>
<div> </div><font color="#888888">
<div>sona<br><br></div></font>
<div>
<div></div>
<div>
<div class="gmail_quote">On Fri, Jan 8, 2010 at 12:53 PM, susumu mori <span dir="ltr"><<a href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">Hi Sona,<br><br>There is detailed description about the "flip" function in the manual. the truth is, nobody is sure about the sign because scanners can change it dynamically depending on your scan protocol.<br>
There is a way to rigorously solve this problem, but it is very difficult and that's why we just empirically solve it by checking all 4 options (no check, x, y, z flipped). Good news is, if the signs are wrong, tracking doesn't make sense.
<div>
<div></div>
<div><br><br>
<div class="gmail_quote">On Fri, Jan 8, 2010 at 10:34 AM, Sona Saksena <span dir="ltr"><<a href="mailto:saksena.sona@gmail.com" target="_blank">saksena.sona@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">
<div>Hi,</div>
<div> </div>
<div>Thanks for your suggestion. There is a option in the fiber tracking parameters "Flip Eigen Vector". Do I have to use this check box?</div>
<div> </div>
<div>Actually we have applied gradients in 26 directions (GE Scanner, 3Tesla). I am not sure about the sign of all of the components in the gradient table. What shall I do?</div>
<div> </div>
<div>This is the gradient table.</div>
<div> </div>
<div>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">0: 0.000000, 0.000000, 0.000000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">1: 1.000000, 0.000000, 0.000000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">2: 0.849000, 0.528000, 0.000000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">3: -0.108000, 0.565000, 0.818000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">4: 0.884000, -0.345000, -0.315000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">5: -0.003000, -0.736000, 0.677000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">6: -0.868000, -0.238000, 0.436000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">7: 0.799000, 0.370000, 0.475000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">8: -0.162000, 0.987000, 0.000000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">9: 0.866000, -0.129000, 0.483000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">10: -0.212000, -0.936000, 0.281000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">11: 0.068000, -0.892000, -0.446000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">12: 0.550000, -0.544000, -0.634000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">13: -0.435000, -0.422000, 0.795000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">14: -0.599000, 0.780000, 0.182000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">15: -0.525000, 0.030000, -0.851000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">16: -0.600000, -0.688000, 0.409000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">17: 0.653000, -0.060000, -0.755000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">18: 0.207000, -0.076000, -0.975000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">19: -0.413000, -0.699000, -0.584000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">20: -0.436000, 0.822000, -0.366000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">21: 0.462000, 0.874000, 0.148000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">22: -0.503000, 0.488000, -0.713000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">23: 0.824000, -0.530000, 0.202000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">24: 0.297000, 0.349000, 0.889000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">25: -0.040000, 0.318000, -0.947000</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"></span> </p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">Please do suggest?</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"></span> </p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">regards</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"></span> </p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">sona</span></p>
<p style="MARGIN: 0in 0in 10pt 0.5in"><font face="Calibri" size="3"> </font></p><br><br></div>
<div>
<div></div>
<div>
<div class="gmail_quote">On Thu, Jan 7, 2010 at 3:32 PM, susumu mori <span dir="ltr"><<a href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">Hi Sona,<br><br>I suggest you to go through the manual section in <a href="http://www.mristudio.org/" target="_blank">www.mristudio.org</a>. There you can find a user's manual for DtiStudio. It gives you the step-by-step procedure for tensor calculation and fiber tracking.<br>
<br>
<div class="gmail_quote">
<div>
<div></div>
<div>On Thu, Jan 7, 2010 at 2:48 PM, Sona Saksena <span dir="ltr"><<a href="mailto:saksena.sona@gmail.com" target="_blank">saksena.sona@gmail.com</a>></span> wrote:<br></div></div>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">
<div>
<div></div>
<div>
<div>Hello,</div>
<div> </div>
<div>Please can you tell me steps of performing fiber tracking in brain tumor patients using DTI studio. The DTI data is on 3T GE scanner with gradients applied in 26 directions. How to generate the reconstructed fibres?</div>
<div> </div>
<div>thanks</div>
<div> </div>
<div>regards</div>
<div> </div><font color="#888888">
<div>Sona Saksena</div>
<div><br> </div></font><br></div></div>_______________________________________________<br>Mristudio-users mailing list<br><a href="mailto:Mristudio-users@mristudio.org" target="_blank">Mristudio-users@mristudio.org</a><br>
<a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>Unsubscribe, send a blank email to: <a href="mailto:Mristudio-users-unsubscribe@mristudio.org" target="_blank">Mristudio-users-unsubscribe@mristudio.org</a><br>
<br></blockquote></div><br><br>_______________________________________________<br>Mristudio-users mailing list<br><a href="mailto:Mristudio-users@mristudio.org" target="_blank">Mristudio-users@mristudio.org</a><br><a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>
Unsubscribe, send a blank email to: <a href="mailto:Mristudio-users-unsubscribe@mristudio.org" target="_blank">Mristudio-users-unsubscribe@mristudio.org</a><br><br></blockquote></div><br><br clear="all"><br></div></div><font color="#888888">-- <br>
Sona Saksena<br>Ph. D Scholar<br></font><br>_______________________________________________<br>Mristudio-users mailing list<br><a href="mailto:Mristudio-users@mristudio.org" target="_blank">Mristudio-users@mristudio.org</a><br>
<a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>Unsubscribe, send a blank email to: <a href="mailto:Mristudio-users-unsubscribe@mristudio.org" target="_blank">Mristudio-users-unsubscribe@mristudio.org</a><br>
<br></blockquote></div><br></div></div><br>_______________________________________________<br>Mristudio-users mailing list<br><a href="mailto:Mristudio-users@mristudio.org" target="_blank">Mristudio-users@mristudio.org</a><br>
<a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>Unsubscribe, send a blank email to: <a href="mailto:Mristudio-users-unsubscribe@mristudio.org" target="_blank">Mristudio-users-unsubscribe@mristudio.org</a><br>
<br></blockquote></div><br><br clear="all"><br>-- <br>Sona Saksena<br>Ph. D Scholar<br></div></div><br>_______________________________________________<br>Mristudio-users mailing list<br><a href="mailto:Mristudio-users@mristudio.org" target="_blank">Mristudio-users@mristudio.org</a><br>
<a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>Unsubscribe, send a blank email to: <a href="mailto:Mristudio-users-unsubscribe@mristudio.org" target="_blank">Mristudio-users-unsubscribe@mristudio.org</a><br>
<br></blockquote></div><br></div></div><br>_______________________________________________<br>Mristudio-users mailing list<br><a href="mailto:Mristudio-users@mristudio.org">Mristudio-users@mristudio.org</a><br><a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>
Unsubscribe, send a blank email to: <a href="mailto:Mristudio-users-unsubscribe@mristudio.org">Mristudio-users-unsubscribe@mristudio.org</a><br><br></blockquote></div><br><br clear="all"><br>-- <br>Sona Saksena<br>Ph. D Scholar<br>