[Mrtrix-discussion] Mrtrix-discussion Digest, Vol 59, Issue 6

Chris Adamson chris.adamson at mcri.edu.au
Sun Dec 8 16:10:17 PST 2013 

I have some python scripts for tck/trk handling.

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Today's Topics:

   1. Re: Mrtrix-discussion Digest, Vol 59, Issue 5 (Nagesh Adluru)


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Message: 1
Date: Fri, 6 Dec 2013 18:03:07 -0600
From: Nagesh Adluru <nagesh.adluru at gmail.com>
To: mrtrix-discussion at www.nitrc.org
Subject: Re: [Mrtrix-discussion] Mrtrix-discussion Digest, Vol 59,
	Issue 5
Message-ID:
	<CAL7GMYQ_c6RQVp_OFKBUcjjgRAszdM7MF-2HCnQ=JNCHzdV7fw at mail.gmail.com>
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Hello Dorian,

You can convert .tck to .trk using our package. It's a bit indirect in that it requires you to install DTI-TK's TractTool but it works. Of course you also need to install the latest camino-trackvis.

Below is the sample script (also available in the download link)

Download link: http://sourceforge.net/projects/camino-trackvis/files/0.2/

#Converting MRTRIX tracts to Trackvis format via VTK.
streamtrack -seed wm_mask-mask.mif -step 2 -cutoff 0.2 -grad encoding.b DT_STREAM dwi.mif roi_tracts.tck tracks2vtk roi_tracts.tck roi_tracts_mrtrix.vtk TractTool -in roi_tracts_mrtrix.vtk -camino roi_tracts_mrtrix.Bfloat mrconvert wm_mask-mask.mif wm_mask-mask.nii camino_to_trackvis -i roi_tracts_mrtrix.Bfloat -o roi_tracts_mrtrix.trk --nifti wm_mask-mask.nii --phys-coords

Hope this helps!

Best,
Nagesh



On Fri, Dec 6, 2013 at 2:00 PM, <mrtrix-discussion-request at www.nitrc.org>wrote:

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> Today's Topics:
>
>    1. Re: Windows version limit in fiber number? (Robert Smith)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 6 Dec 2013 13:33:57 +1100
> From: Robert Smith <r.smith at brain.org.au>
> To: "Dorian P." <alb.net at gmail.com>
> Cc: mrtrix mailinglist <mrtrix-discussion at www.nitrc.org>
> Subject: Re: [Mrtrix-discussion] Windows version limit in fiber
>         number?
> Message-ID:
>         <CAAVKx7Wrzrx4n_1r-L2n6AZ8eU+Ce9wS4X3xx7XO=
> u+NSue7jQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Dorian,
>
> Generally this issue will crop up for one of three reasons:
>
>    - Memory leak in the Windows version of MRtrix. There seems to be an
>    unusual problem when streamtrack is compiled for Windows where the 
> memory
>    used by previously generated streamlines is not properly freed, and the
>    program therefore crashes when it consumes all of your system's RAM. But
>    even if this is not the problem, running the Linux version inside a 
> virtual
>    machine can be considerably faster, and MRtrix was built as a Linux
>    package, so this is our preference.
>    - Use of a 32-bit operating system. The OS can no longer refer to the
>    correct offset in the file, and therefore can't write to the file
>    correctly. The issue will arise as soon as the file size hits 2GB or 4GB
>    (probably the former). My understanding is that there is not yet a 
> working
>    64-bit Windows MRtrix compilation, so the Windows version will encounter
>    this limit regardless of the version of Windows being used. Again, 
> a 64-bit
>    Linux running inside a virtual machine is preferable, though I'm 
> not sure
>    whether you will get access to > 3.25GB of RAM in the virtual machine if
>    your Windows install is natively 32-bit (someone else may be able 
> to answer
>    this question).
>    - Use of a 32-bit file system such as FAT32 on your target hard disk
>    drive. This is particularly common when users try to write their 
> .tck files
>    to an external hard drive.
>
> As to why your system could not open the successful .tck file, it's 
> difficult to know without more information. But the first step is to 
> make sure that your system isn't running out of RAM when loading the file.
>
> For conversion from .tck to .trk, I don't know of any other tools, 
> though I do vaguely recall writing a command to convert the other 
> way... so it can't be too difficult, and somebody on here may already 
> have an appropriate program.
>
> Best regards
> Rob
>
>
> --
>
> *Robert Smith*
> Post-Doctoral Researcher, Imaging Division
>
> The Florey Institute of Neuroscience and Mental Health Melbourne Brain 
> Centre - Austin Campus
> 245 Burgundy Street
> Heidelberg Vic 3084
> Ph: +61 3 9035 7128
> Fax: +61 3 9035 7301
> www.florey.edu.au
>
>
> On Fri, Dec 6, 2013 at 4:47 AM, Dorian P. <alb.net at gmail.com> wrote:
>
> > Hello Donald and other mtrixers,
> >
> > I am using regularly MRtrix in windows without any trouble. The only
> thing
> > that seem to be limited is the number of fibers. I tried to get 1 
> > million fibers and it crashed:
> >  540742 generated,   518411 selected    [ 51%]streamtrack: error writing
> > to tracks file: Invalid argument
> >
> > File was about 2GB. I ran it again with 450,000 fibers and it worked.
> > However, mrview cannot open the .tck file.
> >
> > What is the limit of fiber number in the Windows version? Is it 
> > better in Linux?
> >
> > Also, is there a way to convert .tck to TrackVis .trk file? I found 
> > a python script but needs installation of all sorts of addons that 
> > my computer is not liking.
> >
> > Thank you.
> >
> > Dorian
> > TJU
> >
> > _______________________________________________
> > Mrtrix-discussion mailing list
> > Mrtrix-discussion at www.nitrc.org
> > http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
> >
> >
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