[Mrtrix-discussion] Conversion of 4D analyze file into mif DWi dataset

[Donald Tournier]

Hello Matteo & Marco,

Thijs is probably right, it's most likely that the filesize is too large to
be mapped into your RAM. It's a little annoying that the OS doesn't provide
anything more informative about the error than "no error", but at least we
know it's a failed memory-mapping. I'm surprised this happened with a
filesize of 1GB though.

Can you tell us:
- how much RAM you have installed, and how much swap (type 'free' in a
terminal if using Linux).
- whether you're running the 32-bit or 64-bit version.

On some platforms, the 32-bit version will only handle a maximum of 2GB of
memory mapping, and since you're copying data from a 1GB dataset into
another 1GB dataset, that will probably be enough to go over the limit.
Shouldn't happen on a 64-bit system, unless potentially you run out of
physical memory...

On a separate note: why are you trying to convert the file to mif format?
All MRtrix commands will happily handle your 4D analyse file directly
(memory permitting)...

Cheers,

Donald.



On 20 June 2011 18:23, Thijs Dhollander <thijs.dhollander at uzleuven.be>wrote:

> Hi Matteo & Marco,
>
> I think you might be right about it being a memory error.  I remember
> getting the same error in a different -but then again similar- situation: I
> was performing TDI, but at a pretty high resolution.  The final mif file
> also got created (at what seemed to be the right filesize), but then it gave
> me the same "no error" error.
>
> What you could try in your situation (apart from getting more memory :-)),
> is to import parts of it along some dimensions... if that makes sense for
> what is in your data and what you want to do with it.  For instance, if your
> images have a very high resolution, you could import the upper and lower
> half of them separately.  Or if you just acquired many different b-shells,
> you could import one of them.  Or if you acquired many repetitions, you
> could import them separately and then average them, etc...
>
> Kind regards,
>
> Thijs Dhollander
> PhD Student
>
> thijs.dhollander at uz.kuleuven.ac.be
> tel. +32 16 34 90 37
> gsm. +32 475 36 44 27
>
> Medical Image Computing (K.U.Leuven, ESAT/PSI, MIC)
> Medical Imaging Research Center | UZ Gasthuisberg | Herestraat 49 - bus
> 7003 | B-3000 Leuven | http://www.medicalimagingcenter.be
>
> -----Original Message-----
> From: mrtrix-discussion-bounces at public.nitrc.org [mailto:
> mrtrix-discussion-bounces at public.nitrc.org] On Behalf Of Matteo Figini
> Sent: vrijdag 17 juni 2011 20:14
> To: mrtrix-discussion
> Cc: Marco Castelli
> Subject: [Mrtrix-discussion] Conversion of 4D analyze file into mif DWi
> dataset
>
> Hello
>
> We have a problem in the import of 4D analyze (hdr/img) images into mrtrix
>
> We used the following string:
>      mrconvert name.img dwi.mif
> but we received the following error:
>      mrconvert: memmory mapping filed for file 'dwi.mif': No error
>
> A dwi.mif file of the same size of the img was generated but when we
> checked it with mrview we can't see any image.
> We point out that our img file is about 1GB and we wonder if this could
> generate a memory error.
>
> Matteo and Marco
>
>
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-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9035 7033
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