[Mrtrix-discussion] MRTrix Track visualization - fibernavigator

[Luetzkendorf, Ralf]

Hi all,

did somebody try the fibernavigator.
I hadnt any luck so far.
If I try to load the anatomy changed by MRTrix, it allways breaks. If I change the filetype with FSL, sometimes it works, but its very rar.
Loading the tck file didnt work either. Its a relativly high resolution (1mm iso wholebrain). 1.4mm didnt work either.
Would be great if somebody had any luck or can give me a hint.

Cheers,

Ralf


+++++++++++++++++++++++++++++++++++++++++++++++
Ralf Lützkendorf
Department for Biometry and Medical Informatics
University of Magdeburg, Germany
phone: +49 391 67 13546
fax: +49 391 67 13536

________________________________
Von: mrtrix-discussion-bounces at www.nitrc.org [mrtrix-discussion-bounces at www.nitrc.org]" im Auftrag von "Ivan Alvarez [ivan.alvarez.11 at ucl.ac.uk]
Gesendet: Freitag, 25. April 2014 16:34
An: mrtrix-discussion at www.nitrc.org
Betreff: Re: [Mrtrix-discussion] MRTrix Track visualization

Jean, Fibernavigator looks great! Will have to check it out, thanks for the heads up : )

Kind regards,
Ivan Alvarez

PhD Candidate
Imaging and Biophysics Unit
UCL Institute of Child Health
30 Guilford Street, London, WC1N 1EH

On 25/04/14 14:43, Jean-Christophe Houde wrote:
Dear Ralf,

2 other options are also quite handy:

- You can use the Fibernavigator<https://github.com/scilus/fibernavigator> to display them directly. You only need to load the supporting anatomy before, to correctly get the transformation matrix.
- You can use the Tractconverter<https://github.com/MarcCote/tractconverter> to convert them to some formats that are supported by other applications.

Best regards,

--
Jean-Christophe Houde, M. Sc.
Research assistant
Sherbrooke Connectivity Imaging Lab<http://scil.dinf.usherbrooke.ca/>
Sherbrooke University

Le 14-04-25 06:25, Ivan Alvarez a écrit :
Dear Ralf,

There are a few ways to do this - MRview has a "2.5D" display, which lets you rotate the viewpoint by pressing ctrl+middle mouse button - it's explained in a recent thread on the mailing list.

As for proper 3D renders, you can try converting your streamlines to a format readable by a third party package. People have successfully managed to display streamlines in ParaView<http://www.paraview.org/> via Camino<http://cmic.cs.ucl.ac.uk/camino/index.php?n=Tutorials.DTI> and in TrackVis<http://trackvis.org/> via Nipype<http://nipy.sourceforge.net/nipype/interfaces/generated/nipype.interfaces.mrtrix.convert.html>.

--
Kind regards,
Ivan Alvarez

PhD Candidate
Imaging and Biophysics Unit
UCL Institute of Child Health
30 Guilford Street, London, WC1N 1EH

On 25/04/2014 11:16, Luetzkendorf, Ralf wrote:

Hi MRTrix Fans,

I was wondering if there is a way to visualize the results in 3D. There was a discussion in the forum from 2012.
Is thee any new way or a favorit way to visualize?

Thenaks for the help,

Ralf Luetzkendorf
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