<div dir="ltr"><div>Hello Dorian,<br><br>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.<br>
<br>Below is the sample script (also available in the download link)<br><br></div><div>Download link: <a href="http://sourceforge.net/projects/camino-trackvis/files/0.2/">http://sourceforge.net/projects/camino-trackvis/files/0.2/</a><br>
</div><div><br>#Converting MRTRIX tracts to Trackvis format via VTK.<br>streamtrack -seed wm_mask-mask.mif -step 2 -cutoff 0.2 -grad encoding.b DT_STREAM dwi.mif roi_tracts.tck<br>tracks2vtk roi_tracts.tck roi_tracts_mrtrix.vtk<br>
TractTool -in roi_tracts_mrtrix.vtk -camino roi_tracts_mrtrix.Bfloat<br>mrconvert wm_mask-mask.mif wm_mask-mask.nii<br>camino_to_trackvis -i roi_tracts_mrtrix.Bfloat -o roi_tracts_mrtrix.trk --nifti wm_mask-mask.nii --phys-coords<br>
<br></div><div>Hope this helps!<br></div><div><br></div>Best,<br>Nagesh<br><div><br><div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Dec 6, 2013 at 2:00 PM, <span dir="ltr"><<a href="mailto:mrtrix-discussion-request@www.nitrc.org" target="_blank">mrtrix-discussion-request@www.nitrc.org</a>></span> wrote:<br>
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Today's Topics:<br>
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1. Re: Windows version limit in fiber number? (Robert Smith)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 6 Dec 2013 13:33:57 +1100<br>
From: Robert Smith <<a href="mailto:r.smith@brain.org.au">r.smith@brain.org.au</a>><br>
To: "Dorian P." <<a href="mailto:alb.net@gmail.com">alb.net@gmail.com</a>><br>
Cc: mrtrix mailinglist <<a href="mailto:mrtrix-discussion@www.nitrc.org">mrtrix-discussion@www.nitrc.org</a>><br>
Subject: Re: [Mrtrix-discussion] Windows version limit in fiber<br>
number?<br>
Message-ID:<br>
<CAAVKx7Wrzrx4n_1r-L2n6AZ8eU+Ce9wS4X3xx7XO=<a href="mailto:u%2BNSue7jQ@mail.gmail.com">u+NSue7jQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi Dorian,<br>
<br>
Generally this issue will crop up for one of three reasons:<br>
<br>
- Memory leak in the Windows version of MRtrix. There seems to be an<br>
unusual problem when streamtrack is compiled for Windows where the memory<br>
used by previously generated streamlines is not properly freed, and the<br>
program therefore crashes when it consumes all of your system's RAM. But<br>
even if this is not the problem, running the Linux version inside a virtual<br>
machine can be considerably faster, and MRtrix was built as a Linux<br>
package, so this is our preference.<br>
- Use of a 32-bit operating system. The OS can no longer refer to the<br>
correct offset in the file, and therefore can't write to the file<br>
correctly. The issue will arise as soon as the file size hits 2GB or 4GB<br>
(probably the former). My understanding is that there is not yet a working<br>
64-bit Windows MRtrix compilation, so the Windows version will encounter<br>
this limit regardless of the version of Windows being used. Again, a 64-bit<br>
Linux running inside a virtual machine is preferable, though I'm not sure<br>
whether you will get access to > 3.25GB of RAM in the virtual machine if<br>
your Windows install is natively 32-bit (someone else may be able to answer<br>
this question).<br>
- Use of a 32-bit file system such as FAT32 on your target hard disk<br>
drive. This is particularly common when users try to write their .tck files<br>
to an external hard drive.<br>
<br>
As to why your system could not open the successful .tck file, it's<br>
difficult to know without more information. But the first step is to make<br>
sure that your system isn't running out of RAM when loading the file.<br>
<br>
For conversion from .tck to .trk, I don't know of any other tools, though I<br>
do vaguely recall writing a command to convert the other way... so it can't<br>
be too difficult, and somebody on here may already have an appropriate<br>
program.<br>
<br>
Best regards<br>
Rob<br>
<br>
<br>
--<br>
<br>
*Robert Smith*<br>
Post-Doctoral Researcher, Imaging Division<br>
<br>
The Florey Institute of Neuroscience and Mental Health<br>
Melbourne Brain Centre - Austin Campus<br>
245 Burgundy Street<br>
Heidelberg Vic 3084<br>
Ph: +61 3 9035 7128<br>
Fax: +61 3 9035 7301<br>
<a href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a><br>
<br>
<br>
On Fri, Dec 6, 2013 at 4:47 AM, Dorian P. <<a href="mailto:alb.net@gmail.com">alb.net@gmail.com</a>> wrote:<br>
<br>
> Hello Donald and other mtrixers,<br>
><br>
> I am using regularly MRtrix in windows without any trouble. The only thing<br>
> that seem to be limited is the number of fibers. I tried to get 1 million<br>
> fibers and it crashed:<br>
> 540742 generated, 518411 selected [ 51%]streamtrack: error writing<br>
> to tracks file: Invalid argument<br>
><br>
> File was about 2GB. I ran it again with 450,000 fibers and it worked.<br>
> However, mrview cannot open the .tck file.<br>
><br>
> What is the limit of fiber number in the Windows version? Is it better in<br>
> Linux?<br>
><br>
> Also, is there a way to convert .tck to TrackVis .trk file? I found a<br>
> python script but needs installation of all sorts of addons that my<br>
> computer is not liking.<br>
><br>
> Thank you.<br>
><br>
> Dorian<br>
> TJU<br>
><br>
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</blockquote></div><br></div></div></div></div></div></div>