[Mrtrix-discussion] Windows version limit in fiber number?

[Robert Smith]

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
>
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