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

Tue Jun 21 01:05:42 PDT 2011

We have a 64-bit OS with 4 GB of RAM, but we are working on the 32-bit version of MRtrix because it's the only available for Windows (isn't it?).We will try to use the analyse file without converting it; if there will be again problems of memory, we will move to the Linux 64-bit version.
ThanksMatteo and Marco

----Messaggio originale----

Da: d.tournier at brain.org.au

Data: 21/06/2011 2.55

A: "Thijs Dhollander"<thijs.dhollander at uzleuven.be>

Cc: "mrtrix-discussion"<mrtrix-discussion at public.nitrc.org>

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

Hello Matteo &amp; 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 &amp; 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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