Hi Martin,
Your posts have been helpful, as I've been doing a similar analysis with freesurfer surface ROIs. So just to confirm with you, have you found that surface ROIs are giving you more robust results than when converting to volume ROIs (as described in http://sburns.org/2014/05/03/cortical-tractography-recipe.html), now that you've figured out the meshspace option?
Furthermore, running probtrackx2 on all these surfaces (even when I run all my seeds in parallel on a cluster) take a long time. Have you tried decimating the surfaces (with mris_decimate) and have you found that it deteriorates results? I was planning on decimating to 1/2 or 1/3 of the original amount of vertices to speed up processing time. Because diffusion space is relatively low-res and tracking occurs in diffusion space, I can't imagine losing too much with even 1/3 of the original amount of vertices. I will probably confirm for myself, but just curious if you've tried it yourself.
Finally, if you don't mind me asking, what program did you use to make those visuals of the network? They look great.
Thanks,
Rohan
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