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also... the matrix doesn't actually have to be symmetric. consider trains: most people leaving long island are going into new york city (perhaps 3500 out of 5000) but only a small fraction of those leaving new york are going to long island (perhaps 100/5000). -dh On Tue, 2 Sep 2014, David R. Haynor wrote: > hi jiyang, > > i don't know about the command, but most of the asymmetry in the matrix you > included is just poisson noise. to see this, compute M = (a(i,j) + a(j, > i)/2), and then look at the range [M - 2*sqrt(M), M + 2*sqrt(M)]. most of > the time you'll see that a(i,j) and a(j,i) are both in that range. the rest > of the asymmetry probably arises from the fact that the random walk may not > be perfectly reversible (roundoff, discretization, etc.), although it's > close. > > -dh > > On Wed, 3 Sep 2014, Jiyang Jiang wrote: > >> Dear FSL list, >> >> We aim to generate n-by-n connectivity matrix using probtrackx2 (build >> 507), where n is the number of ROIs segmented using AAL atlas. We came >> across some problems in understanding the parameters and results. Your help >> is very much appreciated! >> >> Currently, we are running the following command: >> >> >> probtrackx2 --network \ >> -x ~/ptx2_nw/seedlist.txt \ >> -l \ >> --onewaycondition \ >> -c 0.2 \ >> -S 2000 \ >> --steplength=0.5 \ >> -P 300 \ >> --fibthresh=0.01 \ >> --distthresh=0.0 \ >> --sampvox=0.0 \ >> --forcedir \ >> --opd \ >> -s ~/ptx2_nw/11004.bedpostX/merged \ >> -m ~/ptx2_nw/11004.bedpostX/nodif_brain_mask \ >> --dir=~/ptx2_nw/probtrackx2_try6 >> >> >> Our questions are: >> >> 1. Is this command correct for generating our ROI*ROI matrix? >> 2. We have tried to run the command a). with --omatrix1, b). with >> --targetmasks=~/ptx2_nw/seedlist.txt, and c). with neither of these two >> flags. The outcomes (fdt_network_matrix) were the same. In Saad’s response >> to one of the previous enquiry >> (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1202&L=fsl&P=R65946&1=fsl&9=A&I=-3&J=on&X=A9C4254AE89C6902A5&Y=neuroimageemaillist%40gmail.com&d=No+Match%3BMatch%3BMatches&z=4), >> if I understand it correctly, --targetmasks seems to record any streamline >> arriving at the first target, regardless whether the streamline continues >> to reach other ROI’s (track no further), whereas for --omatrix1 will record >> the real destination of a fiber tract. For example, in the situation of a >> fiber tract from A, passing through B, to C (A → B → C), --targetmasks >> will record this tract as A → B, whereas --omatrix1 will record A→C. If >> that is the case, I suppose the results of using --omatrix1 and >> --targetmasks should be different, unless there is not any streamline from >> the seed ROI to the target ROI passing through any of the other ROI’s. Is >> that correct? >> 3. In the same thread mentioned above >> (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1202&L=fsl&P=R65946&1=fsl&9=A&I=-3&J=on&X=A9C4254AE89C6902A5&Y=neuroimageemaillist%40gmail.com&d=No+Match%3BMatch%3BMatches&z=4), >> it seems --network will do the same thing as --omatix1, and --stop has the >> same effects as --targetmasks. Can I use --network and --targetmasks at the >> same time to consider each mask as a seed in turn and all other masks as >> stop masks? >> 4. Why the fdt_network_matrix is not symmetric (see below)? >> 5. Does the number in the matrix below represent the number of >> probabilistic streamlines in consideration of the probability of diffusion >> distribution at each voxel on the route? If that is the case, I suppose at >> lease some decimals are expected? >> >> >> 0 2297 52 198 129 9485 1752 76 >> 3821 0 102 78 83 1293 4746 189 >> 32 43 0 4 4435 393 406 1013 >> 232 51 5 0 241 3649 461 34 >> 95 76 4380 383 0 1022 1704 1102 >> 7286 821 231 4542 619 0 4849 238 >> 1757 3395 959 394 1376 6632 0 767 >> 93 228 2947 74 1612 953 614 0 >> >> Sorry for so many questions, and thank you very much for your time! >> >> Kind regards, >> Jiyang >> >