[Mrtrix-discussion] Export MRtrix files

[Luis Morís]

Hi all,

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.

So these are my two cents:

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.

Matlab was very slow in visualization but you could also work with it if
you've no other solution.

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.

As I said maybe some of these things have changed since I worked on this.

Cheers,

Luis.


On Tue, Mar 18, 2014 at 5:00 PM, Donald Tournier <jdtournier at gmail.com>wrote:

> Hi Manuel,
>
> 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:
>
> http://www.nitrc.org/pipermail/mrtrix-discussion/2012-April/000411.html
>
> Cheers,
> Donald.
>
>
>
> On 17 March 2014 17:51, Ivan Alvarez <ivan.alvarez.11 at ucl.ac.uk> wrote:
>
>>  Dear Manuel,
>>
>> 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.
>>
>> There are a couple of options, TrackVis being the obvious one. You may
>> also want to consider Paraview (http://www.paraview.org/), 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.
>>
>> 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 : )
>>
>> Kind regards,
>> Ivan Alvarez
>>
>> PhD Candidate
>> Imaging and Biophysics Unit
>> UCL Institute of Child Health
>> 30 Guilford Street, London, WC1N 1EH
>>
>> On 17/03/14 17:33, Manuel Blesa Cábez wrote:
>>
>> Dear Ivan,
>>
>> 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?
>>
>> 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.
>>
>> Thanks in advance.
>>
>> Best regards,
>>
>> Manuel Blesa
>>
>>
>>
>> _______________________________________________
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>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>
>>
>
>
> --
> *Dr J-Donald Tournier (PhD)*
>
> *Senior Lecturer, **Biomedical Engineering*
>
> *Division of Imaging Sciences & Biomedical EngineeringKing's College
> London*
>
>
> *A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
> Thomas' Hospital, London. SE1 7EH *
> *T: +44 (0)20 7188 7118 ext 53613
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>
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