I posted this thread two weeks ago, but you might missed it. So I am reposting to seek your help on generating connectivity matrix using probtrackx2.
To make a long story short, I am now interested in the answers to the following questions:
1. Is the command below correct for generating a ROI*ROI connectivity matrix?
2. Would you suggest to use --onewaycondition in the command?
3. Shall we average the corresponding items in the connectivity matrix to achieve a symmetrical one?
---------- Forwarded message ----------
From:
Jiyang Jiang <[log in to unmask]>Date: Wed, Sep 3, 2014 at 11:11 AM
Subject: probtrackx2 to generate ROI-by-ROI connectivity matrix
To:
[log in to unmask]Cc: Jiyang Jiang <
[log in to unmask]>
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
