[Mrtrix-discussion] AFD-weighted connectivity

[Roine Timo]

Hello,

Thanks for the great software and the recent prerelease of the new functionalities!

I am doing structural connectivity analyses and plan to also use AFD as the network weight (among other measures). However, I noticed that the tract-level (i.e. fixel-, not voxel-wise) AFD is not implemented in the tck2connectome-function yet. Are there any plans to include AFD-weighting to tck2connectome?

An alternative, but much more complicated approach, is to use tcknodeextract to extract streamlines between all pairs of labels and then use afdconnectivity and output the AFD-values into a text file. However, it seems that tcknodeextract does not work properly. It saves the tck-files and everything looks correct (e.g. some file-sizes are larger than others, so the number of streamlines varies), but when loading the files (e.g. matlab or mrview), no streamlines exist in the files (the data-field has empty matrices for each streamline). I tested this also with a very simple parcellation image and multiple different whole brain tck-files, without effect. Any idea what could be causing this? I managed to circumvent the problem partly by using tckedit instead, but the result will be different, as any part of the tract may now pass through the parcellated region, not just the end-point (i.e. a pass-through behavior instead).

Thanks in advance!

Kind regards,
Timo

P.S. I know that the SIFTed tract-count may be a better measure for the connectivity, but due to a huge amount of data (about 380 datasets), I would prefer to keep all of the tracts instead.

--
Timo Roine
timo.roine at uantwerpen.be
iMinds-Vision Lab
University of Antwerp, Belgium



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.nitrc.org/pipermail/mrtrix-discussion/attachments/20140528/67aa91d2/attachment-0001.html>