<div dir="ltr">Hi Matthieu,<div><div><br></div><div>I think that looks like a fairly impressive delineation already. The issue in this region will be one of susceptibility-induced distortions and signal dropout - not much that can be done without improving the imaging itself. I notice you're using a fairly basic acquisition (32 DW directions, b=1000, 2x2x2 resolution). If you really want to track such a small structure in such a difficult area to image, I think you'll need to increase all of these parameters... At the very least, try increasing the b-value to 2000, the number of directions to 64 (if not more - it's always good to have additional SNR), and potentially try to increase the resolution - although that last one will be difficult to achieve, since increasing the resolution will very quickly worsen your SNR and image distortions. You may be able to overcome some of these difficulties using parallel imaging, but assuming you only have access to product sequences, you may not be able to get much better resolution than what you have already... If you need to compromise, I think I'd go for more directions and a higher b-value over higher spatial resolution. </div></div><div><br></div><div>The other thing to try is reducing the FOD threshold when tracking (the -cutoff option in streamtrack). This might allow the tracking to bridge the gap, but will come at the expense of a lot more noisy tracks in the output. So this would only really work in conjunction with fairly restrictive include/exclude ROIs...</div><div><br></div><div>Otherwise, Ivan is right that much of the discussion has now shifted over to the MRtrix3 forum, but this is still the right place to ask questions related to the 0.2.x version, no problems there. </div><div><br></div><div>Cheers,</div><div>Donald.</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 24 March 2015 at 11:02, Matthieu Vanhoutte <span dir="ltr"><<a href="mailto:matthieuvanhoutte@gmail.com" target="_blank">matthieuvanhoutte@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div><div>Dear experts,<br><br></div>As recommended by Ivan, I will try to include more details on my post. <br><br></div>I am using MRtrix2 et trying to tract facial nerve (VII) from the internal auditory meatus to brainstem. I am using CSD tracking ans SD_PROB as method. My seed ROI have been defined on the T1 anatomical then register on DTI image (32 directions images, b0 = 1000, resolution = 2x2x2).<br><br></div>As you can see in the joined files, facial nerve on the left hemisphere is visible on T1 anatomical (show focus) however my tracking results show a hole (show focus) in the facial nerve tract.<br><br></div>Many thanks in advance for helping !<br><br></div>Best regards, <br></div><div class="gmail_extra"><span class=""><br clear="all"><div><div><div dir="ltr"><div style="font-family:arial;font-size:small">-------------------------------------<br>Matthieu Vanhoutte, MSc<br></div><div style="font-family:arial;font-size:small">Research Engineer - Department of Neuroradiology </div><div style="font-family:arial;font-size:small">Regional University Hospital, Lille, France<br></div></div></div></div>
<br></span><div><div class="h5"><div class="gmail_quote">2015-03-24 11:06 GMT+01:00 Ivan Alvarez <span dir="ltr"><<a href="mailto:ivan.alvarez.11@ucl.ac.uk" target="_blank">ivan.alvarez.11@ucl.ac.uk</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
Hi Matthieu,<br>
<br>
This mailing list has been largely superseded by a Google+ page
here: <a href="https://plus.google.com/communities/111072048088633408015" target="_blank">https://plus.google.com/communities/111072048088633408015</a><br>
<br>
Also, if you would like some advice from the community I would
recommend including the following details in your post: 1) what
exact structure are you attempting to track? A particular branch of
the facial nerve, or the whole thing? 2) what method are you using?
(tracking algorithm, seed/waypoint ROIs, location), 3) what dMRI
acquisition are you using? (resolution, b values, etc.) and most
importantly, 4) what makes you say the results are not convincing?
in other words, what's going wrong?<br>
<br>
Also, since you're writing here I'll guess you are using MRtrix2,
rather than the newer version
(<a href="https://github.com/jdtournier/mrtrix3" target="_blank">https://github.com/jdtournier/mrtrix3</a>), so it's worth pointing that
out too. Some extra detail would make it easier for the experts to
point you in the right direction. Good luck!<br>
<pre cols="72">Kind regards,
Ivan Alvarez
PhD Candidate
Imaging and Biophysics Unit
UCL Institute of Child Health
30 Guilford Street, London, WC1N 1EH</pre><div><div>
<div>On 24/03/2015 09:17, Matthieu Vanhoutte
wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div>
<div dir="ltr">
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<div>Dear MRtrix's experts,<br>
<br>
</div>
I am trying to compute tracts of the facial nerve
(nerve VII). In order to succeed in this, I have tried
different methods but the results aren't still
convincing :<br>
<br>
</div>
1) I tried to compute tracts from one coordinate seed
with radius of 3 mm at the entry area of the facial
nerve at the brain-stem<br>
<br>
</div>
OR<br>
<br>
</div>
2) I tried to compute tracts from one ROI including the
visible facial nerve from T1 image<br>
<br>
</div>
Could you propose me any other method I should try ?<br>
<br>
</div>
Best regards,<br>
<br clear="all">
<div>
<div>
<div>
<div>
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<div>
<div>
<div>
<div>
<div dir="ltr">
<div style="font-family:arial;font-size:small">-------------------------------------<br>
Matthieu Vanhoutte, MSc<br>
</div>
<div style="font-family:arial;font-size:small">Research
Engineer - Department of Neuroradiology </div>
<div style="font-family:arial;font-size:small">Regional
University Hospital, Lille, France<br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
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<br>
<fieldset></fieldset>
<br>
</div></div><pre>_______________________________________________
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</blockquote>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><b><font color="#990000">Dr J-Donald Tournier (PhD)</font></b><br><div><font color="#990000"><br></font></div><i><font color="#990000">Senior Lecturer, </font></i><i><font color="#990000">Biomedical Engineering</font></i><div><i><font color="#990000">Division of Imaging Sciences & Biomedical Engineering<br>King's College London</font></i><div><i><font color="#990000"><br></font></i></div><div><i><font color="#990000"><b style="font-family:Calibri,sans-serif;font-size:15px"><span style="font-size:10pt">A:</span></b><span style="font-family:Calibri,sans-serif;font-size:10pt"> Department of Perinatal Imaging & Health, 1<sup>st</sup> Floor South Wing, St Thomas' Hospital, London. SE1 7EH</span><br></font></i></div><div><i><font color="#990000"><b>T:</b> +44 (0)20 7188 7118 ext 53613</font></i></div></div><div><i><font color="#990000"><b>W:</b> <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></font></i><br></div></div></div>
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