<div dir="ltr">Hi Michael,<div><br></div><div>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.</div>
<div><br></div><div>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: <a href="https://code.google.com/p/mrtrix/source/checkout">https://code.google.com/p/mrtrix/source/checkout</a></div>
<div><br></div><div>Hope this helps!</div><div>Cheers,</div><div><br></div><div>Donald.</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 23 January 2014 17:52, Michael Schirner <span dir="ltr"><<a href="mailto:m.schirner@fu-berlin.de" target="_blank">m.schirner@fu-berlin.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Donald,<br>
<br>
thanks for coming back to me. This post was a follow up to the post I<br>
posted yesterday, I didn't manage to add it to the thread.<br>
<br>
Below is the text of yesterdays post. I'm happy to provide you with the<br>
data if that helps.<br>
<br>
atb,<br>
Michael<br>
<br>
***snip***<br>
Hi Donald et al,<br>
<br>
we encounter some strange behaviour: streamtrack produces very nice<br>
tracks, but it is often the case, that the first voxel of a track is not<br>
one of the specified seed voxel but right next to one (despite using the<br>
'unidirectional' flag).<br>
<br>
We run streamtrack using this command:<br>
streamtrack SD_PROB CSD8.mif -seed seedmask.mif -include targetmask.mif<br>
-mask mask.mif -nomaskinterp -unidirectional -num 1000 tracks.tck<br>
<br>
The dwi data was read in from a DICOM directory, no further processing<br>
except as specified in the mrtrix documentation. All masks were generated<br>
from freesurfer segmentations, stored as NIFTI and converted to mif-format<br>
using mrconvert. After tracking we convert the tck files to vtk files<br>
using one of the mask-files as '-voxel' image. We tried it with and<br>
without adding +1 to each coordinate dimension, in order to get<br>
matrix-cube indices.<br>
<br>
Strangely, when we use masks that contain only a single seed voxel,<br>
everything works just fine, but as soon if we use a larger ROI we<br>
encounter this problem.<br>
<br>
Any help is much appreciated. Thanks!<br>
<br>
Michael<br>
***<br>
<div class="HOEnZb"><div class="h5"><br>
> Hi Michael,<br>
><br>
> I'm not too sure what you mean, so this is just a guess: unless you<br>
> supplied the -unidirectional option to streamtrack, that is the expected<br>
> behaviour - by default, tracks will proceed in opposite directions from<br>
> the<br>
> seed point, so that it ends up somewhere in the middle of the track.<br>
><br>
> Hope that answers the question. If I've got the wrong end of the stick,<br>
> please provide a bit more context...<br>
><br>
> Cheers,<br>
> Donald<br>
><br>
> --<br>
> Dr J-Donald Tournier (PhD)<br>
><br>
> Senior Lecturer, Biomedical Engineering<br>
> Division of Imaging Sciences & Biomedical Engineering<br>
> King's College London<br>
><br>
> A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St<br>
> Thomas' Hospital, London. SE1 7EH<br>
> T: +44 (0)20 7188 7118 ext 53613<br>
> W:<br>
> <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering" target="_blank">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a><br>
><br>
> On 23 Jan 2014 12:38, "Michael Schirner" <<a href="mailto:m.schirner@fu-berlin.de">m.schirner@fu-berlin.de</a>> wrote:<br>
><br>
>> The problem seems to improve when using high-res masks (1mm isotropic).<br>
>> In<br>
>> this case only a smaller fraction of seed-voxels is affected. Seems like<br>
>> there occurs a rounding error at some point. Nevertheless strange that<br>
>> it<br>
>> never occurs when using only single-voxel masks.<br>
>><br>
>> _______________________________________________<br>
>> Mrtrix-discussion mailing list<br>
>> <a href="mailto:Mrtrix-discussion@www.nitrc.org">Mrtrix-discussion@www.nitrc.org</a><br>
>> <a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
>><br>
><br>
<br>
<br>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><b><font color="#990000">Dr J-Donald Tournier (PhD)</font></b><br><div><font color="#990000"><br></font></div><i><font color="#990000">Senior Lecturer, </font></i><i><font color="#990000">Biomedical Engineering</font></i><div>
<i><font color="#990000">Division of Imaging Sciences & Biomedical Engineering<br>King's College London</font></i><div><i><font color="#990000"><br></font></i></div><div><i><font color="#990000"><b style="font-family:Calibri,sans-serif;font-size:15px"><span style="font-size:10pt">A:</span></b><span style="font-family:Calibri,sans-serif;font-size:10pt"> Department of Perinatal Imaging & Health, 1<sup>st</sup> Floor South Wing, St Thomas' Hospital, London. SE1 7EH</span><br>
</font></i></div><div><i><font color="#990000"><b>T:</b> +44 (0)20 7188 7118 ext 53613</font></i></div></div><div><i><font color="#990000"><b>W:</b> <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering" target="_blank">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a></font></i><br>
</div></div>
</div>