[Mrtrix-discussion] tckgen stuck

[basile pinsard]

Hi Robert,
thanks for the quick fix.
I noted your recommendations about github and mif files, I am quite a
newbie to mrtrix and often have to create cross-ni-software pipelines but
will try to use mif for pure-mrtrix pipelines.
Cheers.

basile


On Wed, Jun 25, 2014 at 3:18 PM, Robert Smith <robert.smith at florey.edu.au>
wrote:

> Hi Basile
>
> Thanks for the very informative and helpful report; it made the error much
> easier to locate and fix.
>
> The offending commit
> <https://github.com/jdtournier/mrtrix3/commit/c8e3955811fc05f3406d353028dbf1a5>
> actually relates to code deep within the multi-threading framework.
> In every other use case this change will have had no effect whatsoever,
> but the dynamic seeding framework is far from a 'typical' use case (it's a thing
> of beauty
> <https://github.com/jdtournier/mrtrix3/blob/master/src/dwi/tractography/tracking/exec.h#L78>,
> actually). Following the change in the multi-threading code, the threads
> didn't know when it was time to terminate, and so the command hung at 99%.
>
> I've just pushed a code commit that fixes the problem.
>
> A couple of other quickies since I never get tired of hearing myself type:
>
>    - GitHub (which hosts the MRtrix3 code) has an issue tracking system
>    <https://github.com/jdtournier/mrtrix3/issues?state=open>. If you ever
>    experience behaviour in the new release that you are confident is a bug, or
>    have a great idea for a feature, people are more than welcome to post there
>    if they choose; it also means that you get credit for anything you report /
>    suggest.
>    - I couldn't help noticing the use of compressed NIfTI images... Given
>    I went to the effort of coding it up, I might as well mention that the new
>    version supports .mif.gz images. Solving all your image compression needs
>    without the constraints of a fixed-width header and ambiguous transform :-P
>
> Good <your relevant timezone> everyone
>
> Rob
>
>
> --
>
> *Robert Smith, Ph.D*
> Research Officer, Imaging Division
>
> The Florey Institute of Neuroscience and Mental Health
> Melbourne Brain Centre - Austin Campus
> 245 Burgundy Street
> Heidelberg Vic 3084
> Ph: +61 3 9035 7128
> Fax: +61 3 9035 7301
> www.florey.edu.au
>
>
> On Wed, Jun 25, 2014 at 5:51 PM, basile pinsard <basile.pinsard at gmail.com>
> wrote:
>
>>  Hi MRtrix experts,
>>
>>  running tckgen on a cluster and the nodes are centos 6.5, with this
>> specific set of option:
>>
>>  $ tckgen -force -act 5tt.nii.gz -info -maxlength 250 -nthreads 12
>> -number 10000 -seed_dynamic fod.nii.gz -step 0.2 fod.nii.gz track.tck
>> ....
>> tckgen [INFO]: step size = 0.2 mm
>> tckgen [INFO]: maximum deviation angle = 14.4 deg
>> tckgen [INFO]: minimum radius of curvature = 1.25 mm
>> tckgen [INFO]: iFOD2 internal step size = 0.0666667 mm
>> tckgen [INFO]: opening image "fod.nii.gz"...
>> tckgen [INFO]: rejection sampling will use 7 directions with a ratio of
>> 1.0728 (predicted number of samples per step = 8.0391)
>>    61056 generated,     9984 selected    [ 99%]
>>
>>  it runs until it almost reachs the total count of fibers requested then
>> get stuck there using all the cpu resources allocated with nthreads, it
>> only happens when using seed_dynamic.
>> A slightly earlier version of mrtrix3 (
>> 52617b9f3a4d58f50d0e802d2609bc7fb503da21 ) does not have this bug. Looking
>> at the diff shows mainly changes related to strides but the fod have been
>> generated with the latest version.
>>
>>  thanks for you help.
>>
>>  cheers
>>
>> --
>>  Basile Pinsard
>>
>> *PhD candidate *
>> Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne
>> Universités, UPMC, INSERM, CNRS
>> Unité de Neuroimagerie Fonctionnelle, CRIUGM, Université de Montréal
>>
>
>


-- 
Basile Pinsard

*PhD candidate*
Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne
Universités, UPMC, INSERM, CNRS
Unité de Neuroimagerie Fonctionnelle, CRIUGM, Université de Montréal
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