[Mrtrix-discussion] First voxel of track is not a seed voxel

[Donald Tournier]

Hi Michael,

OK, I figured out what the issue is. The -nomaskinterp only applies to
include, exclude & mask ROIs, but not to the seed ROI (it's a different
section of code that handles this bit). The current seeding strategy is to
find a point at random where the intensity in the mask is higher than 0.5.
When using tri-linear interpolation, if you have a zero voxel with a few
'one' voxels around one of its corner, some of the zero voxel's volume will
end up with intensity higher than 0.5 - just enough to allow a few seed
points to appear within a voxel that wasn't actually part of the mask.

It's nothing to worry about in most cases, since the spurious seeds will be
located no more than a fraction of a voxel outside the ROI. However, if you
really need to ensure that the seed points are strictly located within the
ROI's voxels, then obviously it's a problem. If you need to get rid of that
problem, I've just committed a fix for it, which makes sure the
-nomaskinterp option also applies to the seed ROI. You can get it direct
from the SVN repo on Google Code:
https://code.google.com/p/mrtrix/source/checkout

Hope this helps!
Cheers,

Donald.




On 23 January 2014 17:52, Michael Schirner <m.schirner at fu-berlin.de> wrote:

> Hi Donald,
>
> thanks for coming back to me. This post was a follow up to the post I
> posted yesterday, I didn't manage to add it to the thread.
>
> Below is the text of yesterdays post. I'm happy to provide you with the
> data if that helps.
>
> atb,
> Michael
>
> ***snip***
> Hi Donald et al,
>
> we encounter some strange behaviour: streamtrack produces very nice
> tracks, but it is often the case, that the first voxel of a track is not
> one of the specified seed voxel but right next to one (despite using the
> 'unidirectional' flag).
>
> We run streamtrack using this command:
> streamtrack SD_PROB CSD8.mif -seed seedmask.mif -include targetmask.mif
> -mask mask.mif -nomaskinterp -unidirectional -num 1000 tracks.tck
>
> The dwi data was read in from a DICOM directory, no further processing
> except as specified in the mrtrix documentation. All masks were generated
> from freesurfer segmentations, stored as NIFTI and converted to mif-format
> using mrconvert. After tracking we convert the tck files to vtk files
> using one of the mask-files as '-voxel' image. We tried it with and
> without adding +1 to each coordinate dimension, in order to get
> matrix-cube indices.
>
> Strangely, when we use masks that contain only a single seed voxel,
> everything works just fine, but as soon if we use a larger ROI we
> encounter this problem.
>
> Any help is much appreciated. Thanks!
>
> Michael
> ***
>
> > Hi Michael,
> >
> > I'm not too sure what you mean, so this is just a guess: unless you
> > supplied the -unidirectional option to streamtrack, that is the expected
> > behaviour - by default, tracks will proceed in opposite directions from
> > the
> > seed point, so that it ends up somewhere in the middle of the track.
> >
> > Hope that answers the question. If I've got the wrong end of the stick,
> > please provide a bit more context...
> >
> > Cheers,
> > Donald
> >
> > --
> > Dr J-Donald Tournier (PhD)
> >
> > Senior Lecturer, Biomedical Engineering
> > Division of Imaging Sciences & Biomedical Engineering
> > King'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
> >
> > On 23 Jan 2014 12:38, "Michael Schirner" <m.schirner at fu-berlin.de>
> wrote:
> >
> >> The problem seems to improve when using high-res masks (1mm isotropic).
> >> In
> >> this case only a smaller fraction of seed-voxels is affected. Seems like
> >> there occurs a rounding error at some point. Nevertheless strange that
> >> it
> >> never occurs when using only single-voxel masks.
> >>
> >> _______________________________________________
> >> Mrtrix-discussion mailing list
> >> Mrtrix-discussion at www.nitrc.org
> >> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
> >>
> >
>
>
>


-- 
*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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