<div dir="ltr"><div><div><div><div><div>Daan<br><br></div>Hopefully I get these correct (it's been a while since I've worked with the 0.2 code):<br></div><div><br></div>1. The Hermite interpolation ("Resampler" class) generates samples that are equidistant on the Hermite spline (i.e. in terms of the interpolation coefficient 'mu' for interpolating a point between two samples). So depending on the shape of the spline (and the spacing of the input streamline points), they may not be perfectly equidistant in Euclidean space, but it's not far from it. A non-linear warp field would probably have a larger influence on this non-equidistant-ness than the interpolation step.<br>
<br></div>2. Each tangent of the streamline is normalised (tracks2prob.cpp, lines 328 and 335). So each streamline point within a voxel (post Hermite interpolation) contributes equally to the mean tangent of the streamline within that voxel.<br>
<br></div>In general I wouldn't be too concerned about the preciseness of a DEC TDI map; the colour hue is intended for visualisation and not for quantitative purposes. If however you have an application that demands accurate determination of these tangents, the next major MRtrix release will include the code for my improved streamline mapping method (<a href="http://www.sciencedirect.com.ezp.lib.unimelb.edu.au/science/article/pii/S1053811912011615#appd003">SIFT paper, appendix 3</a>), which can be used in the generation of DEC TDIs (or used for your own purposes). Because it maps the streamline to the voxel edges instead of just 'up-sampling' it, the tangent and the length of the streamline through each voxel are calculated more accurately.<br>
<br></div><div>Any other questions or concerns let me know<br></div>Rob<br></div><div class="gmail_extra"><br clear="all"><div><br>--<br><br>Robert Smith<br>PhD Candidate <br><br>The Florey Institute of Neuroscience and Mental Health<br>
Melbourne Brain Centre - Austin Campus<br>245 Burgundy Street<br>Heidelberg Vic 3084<br>Ph: +61 3 9035 7128<br>Fax: +61 3 9035 7301<br><a href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a><br><span style="font-size:9pt;font-family:"Times New Roman","serif";color:red"></span></div>
<br><br><div class="gmail_quote">On Fri, Jan 18, 2013 at 12:25 AM, Daan Christiaens <span dir="ltr"><<a href="mailto:Daan.Christiaens@esat.kuleuven.be" target="_blank">Daan.Christiaens@esat.kuleuven.be</a>></span> wrote:<br>
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Dear all,
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</div>
<div>I am trying to calculate the colour TDI map of a full-brain track set that was generated in subject space and warped (non-rigidly) to atlas space using the 'normalise_tracks' command. In doing so, however, the distance between successive samples on each
track can change. This got me thinking about the calculation of the colour TDI: as each track contributes to the colour in each voxel it crosses by the average of the tangent vectors in all samples, an unequal distance between successive samples could have
an effect on the colour, especially if the distance between samples also affects the size of the tangent vectors.</div>
<div><br>
</div>
<div>The 'tracks2prob' command allows to specify a resampling factor, which might solve this issue if it would ensure equidistant samples. Thijs and I have been looking at the code to see if this is indeed the case, but we can't quite figure it out. So basically,
I have 2 questions:</div>
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<ol>
<li>Does Hermite interpolation in the tracks2prob command generate samples at equal distance, or will it only add (let's say 5) samples between every pair of original samples?</li><li>Does the distance between successive samples influence the size of the tangent vectors that contribute to the RGB colour? In other words, are the tangent vectors in all samples normalised before averaging, or will samples that are further apart have a larger
contribution to the colour TDI?</li></ol>
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<div>Many thanks and kind regards,</div>
<div><br>
</div>
<div>Daan</div>
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