<div dir="ltr"><div dir="ltr" style="font-size:13px">Hi Ulrike (and all),<div><br></div><div>a) Under standard usage scenarios, the size of the ODF glyphs shouldn't vary massively. This is because if the amplitude of the raw DWI amplitude is scaled up or down, the estimated response function will scale accordingly, such that deconvolution of a single-fibre voxel should always give an integral of 1.0 or thereabouts. So there would need to be something unusual about the derivation of your response function, or scaling of your image subsequent to RF estimation, for CSD to produce a result like that. The only case I can think of where large ODFs come naturally is if you've used tckmap with the -tod option; those need to be scaled explicitly. You could scale your SH images manually using mrcalc before opening them in the viewer, but personally I'd go back to the raw data and figure out where the scaling discrepancy is coming from.</div><div><br></div><div>The primary effect that the scaling will have is the default 0.1 threshold for tracking. Having massive FOD amplitudes is comparable to setting that threshold to zero; so you'll get a fraction more streamline orientation dispersion, and streamlines will be able to track small noisy FOD lobes. I would suggest that this is probably what's causing those inferior-superior streamlines in the CC. It won't have a tremendous effect on SIFT (everything will just scale accordingly), though it will affect the thresholds used during the FOD segmentation process, so noisy FOD lobes will get included in processing.</div><div><br></div><div>b) Looks like you've <a href="http://www.sciencedirect.com/science/article/pii/S1053811914008155" target="_blank">reproduced my result</a> quite nicely. There's a lot of reasons why this seems an entirely plausible attribute of the white matter to me. Long connections give less bandwidth per unit volume than short ones, so for a fixed volume (like the brain) it makes more sense to have lots of short connections. Or if two distant regions require a structural connection, having that connection perform a 'stop-over' along the way provides increased brain connectivity complexity with little metabolic penalty. Indeed in <a href="http://sirl.stanford.edu/newlm/images/9/91/SchuzBraitenberg.pdf" target="_blank">the reference</a> I used to draw the post-mortem comparison in that paper, they light-heartedly compared this property to the <a href="http://en.wikipedia.org/wiki/Zipf%27s_law" target="_blank">Zipf Law</a> of linguistics. Although the dispersion of probabilistic streamlines will contribute to a bias toward shorter connections, I doubt it's the major factor at play here. I also did everything I could to ensure that SIFT does not have an internal bias toward retaining or rejecting streamlines of any particular length; it comes purely from the reconstruction and the image data.</div><div><br></div><div>So next time you see somebody using 25mm as a tracking minimum length, show them that histogram!</div><div><br></div><div>(P.S. If you're using ACT, and doing whole-brain tracking, there's no need to provide a tracking mask using the -mask option; in fact you're better off not, in case the mask causes streamlines to terminate before they ideally should)</div><div><br></div><div>Rob</div></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 Wed, Jan 21, 2015 at 8:02 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 use MRTrix3 to generate streamlines and SIFT for filtering the result.<br>
I noticed two things where I am not sure if the results are right.<br>
<br>
a) I noted that my ODF glyphs appear to be huge when I load them into MRview (glyphs not being normalized to the b0 image, just as you propose). Even if I completely scroll out of the little ODF display window I am not able to see the corpus callosum glyphs completely. Likewise, I have to scale the overlay by at least 0.01 in order to distinguish individual glyphs. Is that normal?<br>
If not, might it be ascribable to the fact that my data contains larger signal amplitudes than yours (you using TrioTim data with b = 3000; me using TrioTim data with b = 1000)? If so, do you see any problems that might arise when I use such huge glyphs for streamline generation and SIFTing?<br>
<br>
b) Using my huge glyphs, I produce 10,000,000 streamlines with tckgen in the following way:<br>
<br>
tckgen -algorithm iFOD2 -step 1.25 -samples 4 -maxlength 250 -number 10000000 -angle 45 -backtrack -force -seed_gmwmi GM_WM_interface.nii.gz -mask WM_mask.nii.gz -act 5tt.mif CSD.nii.gz out.tck<br>
<br>
Plotting the histogram of resulting streamline lengths shows that by far the greatest proportion of these streamlines are really short (I attached histograms of streamline lengths before and after SIFT if you want to check out the distributions).<br>
I go then on using SIFT to reduce the number of streamlines to 1,000,000 - also here, the greatest proportion are very short fibres. By visual inspection I noticed that there remains quite a number of short fibres in superior-inferior direction within the corpus callosum. That seems really wrong... does that correspond to the distribution of streamline lengths and location on your data after SIFT?<br>
<br>
Thank you very much for your help,<br>
<br>
Ulrike<br>
<span class="HOEnZb"><font color="#888888"><br>
--<br>
Max Planck Institute for Human Cognitive and Brain Sciences<br>
Department of Neuropsychology (A220)<br>
Stephanstraße 1a<br>
04103 Leipzig<br>
<br>
Phone: <a href="tel:%2B49%20%280%29%20341%209940%202586" value="+4934199402586">+49 (0) 341 9940 2586</a><br>
Mail: <a href="mailto:kuhl@cbs.mpg.de">kuhl@cbs.mpg.de</a><br>
Internet: <a href="http://www.cbs.mpg.de/staff/kuhl-12160" target="_blank">http://www.cbs.mpg.de/staff/kuhl-12160</a><br>
<br>
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