<div dir="ltr"><div>Hi Donald,</div><div><br></div><div>I was trying to adapt the parameters to my dataset (mouse brain), but after all the standard parameters show the best results. There are any parameter that I can play to obtain the best results? or the standard values show us the best results? Thanks</div>
<div><br></div><div>Regards,</div><div><br></div><div>Manuel Blesa</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-06-03 19:51 GMT+02:00 Donald Tournier <span dir="ltr"><<a href="mailto:jdtournier@gmail.com" target="_blank">jdtournier@gmail.com</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Hi Manuel,</p>
<p dir="ltr">Any particular reason for the non default parameters for the tracking? These values would be appropriate for iFOD1, but iFOD2 expects larger step sizes and much larger angles. In fact, your angle parameter is itself far too small - value are in degrees, not radians. A sensible value for iFOD1 would be 10 or 20, larger again for iFOD2. Try using the defaults for everything, see if that still produces odd results.</p>
<div class="im HOEnZb">
<p dir="ltr">Cheers,<br>
Donald</p>
<p dir="ltr">--<br>
Dr J-Donald Tournier (PhD)</p>
<p dir="ltr">Senior Lecturer, Biomedical Engineering<br>
Division of Imaging Sciences & Biomedical Engineering<br>
King's College London</p>
<p dir="ltr">A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St Thomas' Hospital, London. SE1 7EH<br>
T: <a href="tel:%2B44%20%280%2920%207188%207118%20ext%2053613" value="+442071887118" target="_blank">+44 (0)20 7188 7118 ext 53613</a><br>
W: <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering" target="_blank">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a><br>
</p>
</div><div class="HOEnZb"><div class="h5"><div class="gmail_quote">On 3 Jun 2014 18:29, "Manuel Blesa Cábez" <<a href="mailto:mblesac@gmail.com" target="_blank">mblesac@gmail.com</a>> wrote:<br type="attribution">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div>Hi Donald,</div><div><br></div><div>I used for all the steps of the reconstruction of thr ODFs MRtrix3. </div><div><br></div><div>The command line that I used is </div><div><br></div><div>dwi2response dwi.mif response.txt -mask mask.mif -grad ag140113a_6_HARDI_KO_ref.b -lmax 8</div>
<div><br></div><div>dwi2fod dwi.mif response.txt fod.mif -mask mask.mif -grad ag140113a_6_HARDI_KO_ref.b -lmax 8</div><div><br></div><div>tckgen fod.mif tracks2_CC1_27.tck -algorithm iFOD2 -grad ag140113a_6_HARDI_KO_ref.b -seed_image roi2_CC1_27.mif -mask mask.mif -number 10000 -step 0.14 -minlength 7 -angle 0.70</div>
<div><br></div><div>The voxelsize is 1.4x1.4x2.8</div><div><br></div><div>With the ODF viewer I can't see any strange. I changed the algorithm to SD_stream and I think that the result is good. Thanks in advance.</div>
<div><br></div><div>Regards,</div><div><br></div><div>Manuel Blesa</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-06-03 18:46 GMT+02:00 Donald Tournier <span dir="ltr"><<a href="mailto:jdtournier@gmail.com" target="_blank">jdtournier@gmail.com</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Hi Manuel,</p>
<p dir="ltr">Yes, iFOD1 is almost identical to streamtrack's SD_PROB. I'm surprised you're getting unrealistic results with either iFOD1 or iFOD2 though, they have both been working well for years now with default parameters. Are you sure you don't have similar issues using the same data set with streamtrack? There is the slight issue that the FODs would need to be either converted using sh_basis or computed separately for each command due to the change in SH basis, but I wouldn't expect even that to cause grossly unrealistic results. Do the FODs obtained using dwi2fod look convincing when displayed in MRView's ODF display tool? Maybe it would help of you posted the commands you used to generate the FOD images and for the tracking, and also provide some information as to the data acquisition parameters?</p>
<p dir="ltr">Cheers,<br>
Donald<br>
<br>
--<br>
Dr J-Donald Tournier (PhD)</p>
<p dir="ltr">Senior Lecturer, Biomedical Engineering<br>
Division of Imaging Sciences & Biomedical Engineering<br>
King's College London</p>
<p dir="ltr">A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St Thomas' Hospital, London. SE1 7EH<br>
T: <a href="tel:%2B44%20%280%2920%207188%207118%20ext%2053613" value="+442071887118" target="_blank">+44 (0)20 7188 7118 ext 53613</a><br>
W: <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering" target="_blank">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a><br>
</p>
<div class="gmail_quote"><div><div>On 3 Jun 2014 17:20, "Manuel Blesa Cábez" <<a href="mailto:mblesac@gmail.com" target="_blank">mblesac@gmail.com</a>> wrote:<br type="attribution"></div></div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div>
<div dir="ltr">Dear all,<br><br>I have a little question about the different propagation algorithms:<br><br>I Know the difference between iFOD and iFOD2, but I would like to know which is the difference between this last algorithms of MRtrix 3 and the SD_PROB of MRtrix 2. I believe that the iFOD1 is the same of SD_PROB, I'm right about this?<br>
<br>In order to perform a realistic tractography, which should I use? because I tried iFOD1 and iFOD2 and I obtained very unrealistic results, maybe is for the parameters that I choosed, but I'm not sure. Thanks in advance.<br>
<br>Best regards,<br><br>Manuel Blesa<br><div><div><div><div><br></div></div></div></div></div>
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