[Mrtrix-discussion] On trials parameter in streamtrack

[J-Donald Tournier]

Whoops, sorry about that typo in your name...

On 17 June 2015 at 11:56, J-Donald Tournier <jdtournier at gmail.com> wrote:

> Hi Alessandra
>
>
>> I was wondering how streamtrack work in generating and selecting tracks.
>> As far as I could see from mailing list, number of streamlines generated
>> are usually higher than actually selected. Both commands can be set by
>> -maxnum and -number options.
>> Reasons for excluding a streamline depend basically on tract length,
>> inclusion or exclusion rois used.
>> To get somehow a sense of the probability to get a connection one could
>> divide number of selected streamlines to the number of generated ones.
>>
>
> Yes, that is one option, but I'd stress that you really want to avoid any
> interpretation of that number as a measure of actual probability. This is
> the reason why Geoff Parker talks about a probabilistic index of
> connectivity (PICo) <http://www.ncbi.nlm.nih.gov/pubmed/12884338> rather
> than actual probabilities - there are far too many factors that come into
> it, see for example Derek Jones' excellent paper on the topic
> <http://www.ncbi.nlm.nih.gov/pubmed/22846632>.
>
>
>> Looking at the messages in the archives, during probabilistick tracking,
>> seed points are randomly selected within the seed mask, then a direction is
>> chosen and eventually stream process starts if amplitude in that direction
>> is higher than initcutoff.
>> From my point of view an approach where a certain number of attempts are
>> made from each voxel in brain mask would make a lot of sense to provide
>> meaningful probability results related to "existence" of a connection;
>> giving the opportunity to choice output number could be potentially
>> dangerous, expecially when making connectomics analyses.
>>
>
> Well, I'd disagree to some extent with the word 'meaningful' in this
> context, but yes, this is a common request. This option is actually
> available in MRtrix3 (along with lots of other approaches to seeding).
> Unfortunately, we have no plans to back-port that feature to the MRtrix 0.2
> version.
>
>
>> I see there exists an option in streamtrack, -trials. How it does work
>> precisely?
>> I tried with a single voxel seed, fixing maxnum and number (100 or 500)
>> and varying trials parameter. Considering i have set a negligible cutoff
>> for minlength (1mm), what i see is that results strongly depend on trials
>> parameter. Really small trials (5) cause all tracts terminating quite close
>> to seed point; with higher number of trials, results get better. On the
>> other side, the larger this number, the higher the likely to get spurious
>> connections.
>> Is it correct to say, due to request of a certain number of streamlines,
>> a lot of seed points are initializied within that unique seed voxel, and
>> only after that trial parameter gets effective?
>>
> I am asking because I am not interested in making whole brain analysis,
>> hence I want to carefully inspect how these parameters work. In the light
>> of that, what could be a good compromise when handling trials, number and
>> maxnum parameters?
>>
>
> The -trials option is unrelated to what you're interested in - it's to do
> with the rejection sampling used during probabilistic tracking, and really
> shouldn't need to be adjusted. What you want in this scenario is to set
> -maxnum and -number to the same value.
>
>>
> I would say if you need finer control over the seeding strategy, you'll
> want to try MRtrix3 <https://github.com/MRtrix3/mrtrix3> instead. And if
> you're seriously interested in connectomics, I recommend you think about
> including ACT <http://www.ncbi.nlm.nih.gov/pubmed/22705374> & SIFT
> <http://www.ncbi.nlm.nih.gov/pubmed/23238430> to generate connectomes
> with meaningful track counts - both of which are available in MRtrix3 and
> documented in their respective wiki entries (ACT
> <https://github.com/MRtrix3/mrtrix3/wiki/Anatomically-Constrained-Tractography-%28ACT%29>,
> SIFT <https://github.com/MRtrix3/mrtrix3/wiki/SIFT>), along with our recommendations
> regarding connectomic analysis
> <https://github.com/MRtrix3/mrtrix3/wiki/Structural-connectome-construction>
> .
>
> Hope that helps,
> Donald.
>
>
>
>>
>> Best,
>> Alessandro
>>
>> --
>> Alessandro Calamuneri, M.Sc., PhD
>> Department of Neurosciences, University of Messina, Italy
>>
>>
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>>
>>
>
>
> --
> *Dr J-Donald Tournier (PhD)*
>
> *Senior Lecturer, **Biomedical Engineering*
>
> *Division of Imaging Sciences & Biomedical EngineeringKing's College
> London*
>
>
> *A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
> Thomas' Hospital, London. SE1 7EH*
> *T: +44 (0)20 7188 7118 ext 53613*
> *W: http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
> <http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering>*
>



-- 
*Dr J-Donald Tournier (PhD)*

*Senior Lecturer, **Biomedical Engineering*

*Division of Imaging Sciences & Biomedical EngineeringKing's College London*


*A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
Thomas' Hospital, London. SE1 7EH*
*T: +44 (0)20 7188 7118 ext 53613*
*W: http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
<http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering>*
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