[Mrtrix-discussion] Ubuntu Virtual Machine - Error Message after loading Whole Brain Track

[Donald Tournier]

Hi Ralf,

Difficult to know what's going on without a bit more information, but my
guess is things start going wrong when you hit the 32-bit threshold. I'm
not sure why it wouldn't at least stop tracking if that were the case
though, I thought I'd put in some checks in case this type of  problem
occurred... In any event, the fact that you can generate a decent number of
tracks successfully strongly suggests that the problem is related to file
size in some way, and a quick calculation suggests that 500,000 tracks
would probably take up of the order of 2-4Gb. You can probably check
whether your file grows as expected beyond 2 or 4Gb: if it stops at that
point, that would be the problem...

Assuming that's the case, the problem would be either that you're running a
32 version of MRtrix, that your virtual machine is itself 32 bit, or that
the filesystem you're writing to doesn't support large file sizes (e.g. the
FAT filesystem as used in DOS-formatted hard drives). Since it does look
like you're writing to an external hard drive, I would have a good look at
how it's formatted... If it's a FAT partition, you might want to consider
reformatting as a NTFS partition.

Hope this helps,
Donald.


--
Dr J-Donald Tournier (PhD)

Senior Lecturer, Biomedical Engineering
Division of Imaging Sciences & Biomedical Engineering
King'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
W:
http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering

On 13 Jan 2014 13:53, "Ralf" <luetzken at med.ovgu.de> wrote:

> Hello,
>
> did somebody encounter the error?
>
> I can load whole brain tracks with 500,000 but 1,000,000 and above doesnt
> work.  Im not sure where the threshold is.
>
> Terminal:
>
> generated the track:
>
> 30111  405207 generated,
> 30111 2019750 generated,
> 1500000 selected    [100%]
> [1]+  Done
>
> real 68m21.159s
> user 61m49.668s
> sys 7m42.241s
>
> ubuntu at ubuntu-virtual-machine:/mnt/hgfs/HR_DWI/ho33_2404_1.4_B1500_ElectroVectorScheme/dicomdaten_nr3538$
> mrview anat_ho33_2404.mif &[1] 4237
>
> Then I try loading the Track with the GUI:
>
> ubuntu at ubuntu-virtual-machine:/mnt/hgfs/HR_DWI/ho33_2404_1.4_B1500_ElectroVectorScheme/dicomdaten_nr3538$
> mrview: file
> "/mnt/hgfs/HR_DWI/ho33_2404_1.4_B1500_ElectroVectorScheme/dicomdaten_nr3538/whole_brain_1500000t.tck"*
> is not in MDS format (unrecognised magic number)*
>
> No further details about the error are given.
>
> Hope somebody can help,
>
> Ralf Lützkendorf
>
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>
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