<div dir="ltr">Hi Ulrike (and all),<div><br></div><div>After submitting that manuscript and experimenting more with the raw data, I ended up changing my mind about the whole white matter fraction path integral calculation in ACT.</div><div>The theory was to allow very short streamlines that confidently passed through white matter, but require a longer length from streamlines that consistently pass through areas with partial volume with other tissues... I liked the concept, but in practise it introduced some issues: </div><div><ul><li>Where there was an absence of short reconstructed streamlines, it was difficult to tell whether streamline rejection was caused by this criterion or some other mechanism;</li><li>Without densely up-sampling the streamlines (which would be costly), the result of the path integral calculation could vary depending on exactly where the streamline points lay within the sub-voxel volume;<br></li><li>Without a clear tangible benefit, it was kind of disobeying Occam's Razor.</li></ul><div>The current default tckgen behaviour is as follows: The minimum length is automatically set to 5 voxels, <i>unless</i> ACT is used, in which case it defaults to 2 voxels; either of these is over-ridden using the -minlength option. The white matter fraction path integral calculation is disabled by default. There's a pseudo-justification for the 2-voxel-length threshold in the <a href="http://www.sciencedirect.com/science/article/pii/S1053811914008155">SIFT follow-up paper</a>.</div><div><br></div><div>If you want to play with it, the path integral method is still there in the code, it's just not accessible from the command-line. You can change the values by directly modifying file src/dwi/tractography/ACT/act.h, lines 33 & 34, then recompiling: The first is the white matter fraction path integral threshold, the second is a threshold applied to the maximum WM partial volume fraction along the streamline (bear in mind that it's a trilinear-interpolated value read at each point). The standard minimum length criterion will be applied also unless you specify -minlength 0.</div></div><div><br></div><div>Would like to hear about any tests you perform, or whether anybody has particularly strong views on the topic.</div><div>Rob</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><br>--<br><br><span style="color:rgb(255,102,0)"><b>Robert Smith, Ph.D</b><br>Research Officer, Imaging Division</span><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></div></div></div>
<br><div class="gmail_quote">On Mon, Dec 22, 2014 at 10:00 PM, Ulrike Kuhl <span dir="ltr"><<a href="mailto:kuhl@cbs.mpg.de" target="_blank">kuhl@cbs.mpg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear MRTrix team,<br>
<br>
I want ot use anatomically constrained tractography as explained in the Smith (2012) paper using the 'tckgen -act ...' command.<br>
However, I'm a little unsure about the minimum streamline length option: if I do not call 'tckgen -act ...' with a specified '-minlength' option, does the algorithm automatically use the white matter fraction path integral criterion as explained in Smith (2012)?<br>
<br>
Thank you very much for your help!<br>
All the best and have a happy Christmas!<br>
<br>
Ulrike<br>
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