[Mrtrix-discussion] Sreamtrack error

Tue May 7 16:49:36 PDT 2013

Oops, sorry I forgot to add a practical issue to have in mind: mradd needs
that all the TDIs must have the same FOV. Therefore, if you do the first
TDI with the -vox option (in tracks2prob), and all the other ones using
this first TDI for the -template option (in tracks2prob), then it should be
okay.
Fernando

----------------------------------------
*A/Prof. Fernando Calamante*
The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
245 Burgundy Street
Heidelberg, Victoria 3084
Australia
Ph: (+61 3) 9035 7041
Fax:   (+61 3) 9035 7307
Email: fercala at brain.org.au

On Wed, May 8, 2013 at 9:45 AM, Fernando Calamante <fercala at brain.org.au>wrote:

> Hi Matteo,
> To add my two cents, if what you are interested is in doing TDI, then you
> can just break your tracking in smaller chunks and then use mradd to add
> the TDIs. In other words, (for example) the results for these 2
> cases should be exactly the same:
> 1) create 5M tracks and then do TDI of the 5M file, or
> 2) create 5 separate 1M track files, create their 1M TDIs, and then add
> the 5 TDIs.
> So, although this doesn't solve the problem of the 2GB limit you have, it
> is just a work around for the specific case of TDI :)
> In fact, that is exactly what I do when I have to decide how many tracks
> to use for a given super-resolution (I keep on adding extra TDIs, until I
> get to a contrast-to-noise ratio that is okay for my application).
> Good luck!
> Fernando
>
>
>
> ----------------------------------------
> *A/Prof. Fernando Calamante*
>
> The Florey Institute of Neuroscience and Mental Health
> Melbourne Brain Centre - Austin Campus
> 245 Burgundy Street
> Heidelberg, Victoria 3084
> Australia
> Ph: (+61 3) 9035 7041
> Fax:   (+61 3) 9035 7307
> Email: fercala at brain.org.au
>
>
> On Tue, May 7, 2013 at 6:21 PM, Matteo Diano <matteo.diano at gmail.com>wrote:
>
>> Hi Jeurissen and Donald,
>> thank you very much for your helpfulness. I am going to try to install
>> MRtrix in Centos.
>> Cheers
>>
>> Matteo
>>
>>
>>
>> 2013/5/7 Jeurissen Ben <Ben.Jeurissen at ua.ac.be>
>>
>>>  As Donald explained, MRtrix on Windows is compiled as a 32-bit
>>> executable. A default 64-bit Windows installation will only allow you to
>>> address 2 GB of ram (
>>> http://msdn.microsoft.com/en-us/library/windows/desktop/aa366778(v=vs.85).aspx).
>>> This is why streamtrack fails as soon as your file reaches 2GB of size.
>>>
>>>  A 64-bit Windows executable would solve this issue, but unfortunately
>>> I haven't been able to get the visualization part of mrtrix working
>>> properly in a 64-bit version on Windows...
>>>
>>>  Currently, the only way around this is to use the 64-bit Linux or
>>> MacOS version.
>>>
>>>  Hopefully, future releases will include a 64-bit version on Windows.
>>>
>>>
>>>
>>>     ------------------------------
>>> *From:* mrtrix-discussion-bounces at public.nitrc.org [
>>> mrtrix-discussion-bounces at public.nitrc.org] on behalf of Matteo Diano [
>>> matteo.diano at gmail.com]
>>> *Sent:* 07 May 2013 09:37
>>> *To:* Donald Tournier
>>> *Cc:* mrtrix mailinglist
>>> *Subject:* Re: [Mrtrix-discussion] Sreamtrack error
>>>
>>>    Hi Donald,
>>>  thank you for your answer. I am working on SSD formatted in NTFS with
>>> 16G of RAM and the size of the file is around 2G. So I have no idea about
>>> this issue.
>>>  Cheers
>>>
>>>  Matteo
>>>
>>>
>>> 2013/5/7 Donald Tournier <d.tournier at brain.org.au>
>>>
>>>> Hi Matteo,
>>>>
>>>>  Sounds to me like you've hit a file size limit. What is the size of
>>>> the tracks file when it fails? It might be due to the 32-bit 4GB boundary
>>>> (MRtrix on Windows is compiled as a 32-bit executable, as far as I know),
>>>> but it could also be due to a limitation of your filesystem. Are you
>>>> writing the tracks to a NTFS partition, or a FAT partition? If the latter,
>>>> you'll definitely encounter issues like you describe...
>>>>
>>>>  Hope this helps,
>>>>
>>>>  Donald.
>>>>
>>>>
>>>>
>>>>
>>>>  On 7 May 2013 16:49, Matteo Diano <matteo.diano at gmail.com> wrote:
>>>>
>>>>>    Dear MRtrix experts,
>>>>>  I tried to use streamtrack SB_PROB to obtain the whole brain tracking
>>>>> to fed into the TDI processing (so more than 1 million fibers). Every time
>>>>> I got this error: "973180 generated,   772168 selected    [
>>>>> 19%]streamtrack: error writing to tracks file: Invalid argument". I tried
>>>>> to change data but i had the same problem and it always stops around 18
>>>>> percent. I am using MRtrix on win 7 64b.
>>>>>  Thank you very much!
>>>>>  Regards
>>>>>
>>>>>  Matteo
>>>>>
>>>>>
>>>>>  _______________________________________________
>>>>> Mrtrix-discussion mailing list
>>>>> Mrtrix-discussion at www.nitrc.org
>>>>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>>>>
>>>>>
>>>>
>>>>
>>>>  --
>>>> *Dr Jacques-Donald Tournier
>>>> *
>>>> Research Fellow
>>>>
>>>>  The Florey Institute of Neuroscience and Mental Health
>>>> Melbourne Brain Centre - Austin Campus
>>>> 245 Burgundy Street
>>>> Heidelberg  Vic  3084
>>>> Ph:  +61 3 9035 7033
>>>> Fax:  +61 3 9035 7307
>>>> www.florey.edu.au
>>>>
>>>>
>>>
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>>>
>>
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