<div dir="ltr">Hi all,<div><br></div><div>I'm no longer up to date in tractography but I was working with mrtrix a couple of years ago and faced some of your problems before.</div><div><br></div><div>So these are my two cents:</div>
<div><br></div><div>Paraview did the job for me in visualization, you could colour the streamlines, change the shape etc, if you are looking for a nice image of your data. You could also select to render or not your data so you'll only see a 'draft' of it (Sorry if my terminology is not very professional) making things a bit faster, you could also load nii files with a plugin and superimpose or colour your fibers with those values, etc. Though Paraview had a bit of a learning curve.</div>
<div><br></div><div>Matlab was very slow in visualization but you could also work with it if you've no other solution.</div><div><br></div><div>And if you have enough fibers in your file and just want to make some sanity checks you could just randomly a bunch of fibers from the file, I worked with 10 mill fibers approx, so I took 1 mill or so, to check that everything looked normal.</div>
<div><br></div><div>As I said maybe some of these things have changed since I worked on this.</div><div><br></div><div>Cheers,</div><div><br></div><div>Luis.</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Tue, Mar 18, 2014 at 5:00 PM, Donald Tournier <span dir="ltr"><<a href="mailto:jdtournier@gmail.com" target="_blank">jdtournier@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">Hi Manuel,<div><br></div><div>I don't use the VTK format at all, but from my limited exposure to it, it seems very wasteful (just ran a quick test: 412MB mrtrix track file -> 1.2GB vtk track file), which might explain why you're ending up with such a large file size. In any case, maybe you can get by with MRView's limited 3D display capabilities? I freely admit that they're very poorly documented, but if you follow these instructions, you might find it's sufficient for your needs:</div>
<div><br></div><div><a href="http://www.nitrc.org/pipermail/mrtrix-discussion/2012-April/000411.html" target="_blank">http://www.nitrc.org/pipermail/mrtrix-discussion/2012-April/000411.html</a><br></div><div><br></div><div>
Cheers,</div><div>
Donald.</div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 17 March 2014 17:51, Ivan Alvarez <span dir="ltr"><<a href="mailto:ivan.alvarez.11@ucl.ac.uk" target="_blank">ivan.alvarez.11@ucl.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Dear Manuel,<br>
<br>
The size of the file is dependent on how many streamlines you
generated in MRtrix in the first place. Trackvis may have some
built-in limit on the number of streamlines it can render, you may
want to read the Trackvis documentation for that.<br>
<br>
There are a couple of options, TrackVis being the obvious one. You
may also want to consider Paraview (<a href="http://www.paraview.org/" target="_blank">http://www.paraview.org/</a>), but
it's not something I've yet tried. I think someone suggested using
Camino for the file conversion, so it might be worth exploring.<br>
<br>
In the future, please post these questions to the mailing list;
you have a better chance of getting an answer from an expert (ie.
not me) and others can benefit from the answers as well : )<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>
On 17/03/14 17:33, Manuel Blesa Cábez wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Dear Ivan,<br>
<br>
I read your response to my doubt on the MRtrix forum. I
converted the image with the script that you told me, but the
converted image is very big (8'1GB) and the trackvis can't open
it. Do you know how to solve it?<br>
<br>
Another question: I want to view the MRtrix images in 3D and I
don't know with is the best program to get a 3D visualisation.
Could you recommend me something? Any help will be grateful.<br>
<br>
Thanks in advance.<br>
<br>
Best regards,<br>
<br>
Manuel Blesa<br>
</div>
</blockquote>
<br>
</div>
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<br></blockquote></div><span class="HOEnZb"><font color="#888888"><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><b><font color="#990000">Dr J-Donald Tournier (PhD)</font></b><br><div><font color="#990000"><br>
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