Hi,

I'm trying to reconstruct a structural network to perform some graph analysis with NBS.
I used PANDA to reconstruct the network using probabilistic tractography, now i was giving the input in the NBS software.

I guess as connectivity matrix I have to give the output of probtractX, my question is about the nodes coordinates, I did a 90 seed parcellation using the AAL template.

In the reference manual of NBS i read that there is a script getCOG which assign a coordinate to each seed of the AAL template but it consider the whole template, how can I give only the 90 seed which I used, should I gave as imput my parcellated image? if yes how can I do so?
Sorry for the probable trivial question.

best,
Mauro

Hi Mauro,

When you say you are only using 90 nodes of the AAL, I assume that you have excluded the last 26 nodes in the AAL associated with the cerebellum and vermis. If this is the case, you don't need to run getCOG. You can use /AAL/aalLABELS.txt as your node labels file and /AAL/aalCOG.txt as your COG file. However, make sure that you open these two files in a text editor before using them an delete the last 26 rows. In particular, delete the last 26 coordinates in aalCOG.txt and then delete the last 26 node labels in aalLABELS.txt. Be sure not to leave any blank/empty lines after deleting. Note that aalLABELS.txt and aalCOG.txt are included in the directory called AAL.Once you have delete the last 26 rows, save the files and then specify them in the NBS GUI as usual.

If the set of nodes that you have excluded is more complicated (i.e. not the last 26 nodes; cerebellum & vermis), then please let me know and I can provide some solutions.

Andrew