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

[Ralf]

Hi Donald,


thanks for the answer.

At first Host and Guest system are 64bit and using NTFS and ext4.

The VMWare uses 4GB RAM.


4GB RAM:


700,000 works 2.1 GB

800,000 didn't work 2,33 GB not viewable, and doesn't work for TDI


I raised the RAM to around 6GB:


850,000 works 2,48

1,000,000 works 2,91

1,500,000 works 4,37 not viewable, but works for TDI

2,000,000 works  5,83 not viewable, but works for TDI



What I don't understand is. You dont need RAM for creating the file. But
you need a lot RAM for viewing the file. If you watch the RAM load with
MRView it fits, and if load a file with the 6GB RAM and its to much it goes
near 100% and the terminal kills the process. Thats fine with me. But with
4GB RAM .. the files, that overloads the RAM by viewing...these files
doesnt show the RAM load up. Instead it doesnt even start loading the RAM,
it breaks with (*is not in MDS format (unrecognised magic number).*

Also, if I try to calculate TDI the same error message is thrown.


So far, I have no limits for the 6GB RAM and the TDI processing. Viewing
breaks between 1,000,000 between 1,500,000.


Its fine with me, I can raise the RAM or playing with the SWAP file. But
I'm curious about it. Maybe there is an easy answer or it helps somebody
else.


**********************************************************************




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<https://exmail.med.uni-magdeburg.de/owa/redir.aspx?C=6L5TSjZ7GEqdCag4y93XoyXbV5Kb5NAIAHJqEQfU-6Bpo1SU6NsXe3_85akimfXLSlXNiSAwvZI.&URL=http%3a%2f%2fwww.kcl.ac.uk%2fmedicine%2fresearch%2fdivisions%2fimaging%2fdepartments%2fbiomedengineering>

On 13 Jan 2014 13:53, "Ralf"
<luetzken at med.ovgu.de<https://exmail.med.uni-magdeburg.de/owa/redir.aspx?C=6L5TSjZ7GEqdCag4y93XoyXbV5Kb5NAIAHJqEQfU-6Bpo1SU6NsXe3_85akimfXLSlXNiSAwvZI.&URL=mailto%3aluetzken%40med.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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