[Mrtrix-discussion] Sreamtrack error

Matteo Diano matteo.diano at gmail.com
Wed May 8 00:00:23 PDT 2013


Hi Fernando,
thank you very much for your suggestions! Now i have installed MRtrix in
Ubuntu and it seems to work great. I used 4M but now i know that i could
add more tracks instead repeat the entire estimation. :)
Cheers

Matteo


2013/5/8 Fernando Calamante <fercala at brain.org.au>

> 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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>>
>
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