First, a slight correction to my previous reply: the command is -cifti-correlation, but you seem to have figured that out.
The HCP data is in Cifti files, and contain combined surface (for cortex) and voxel (for subcortical structures and cerebellum) data. The surfaces used have roughly equivalent spacing to the voxels used, so in some sense it is at the voxel "scale". However, two thirds of the data is not in voxels, but in surface vertices. Yes, it is a complete connectivity matrix, hence the large size. Connectome Workbench ( http://www.humanconnectome.org/software/connectome-workbench.html) is the main tool we use with cifti files, you can visualize the data with the GUI, or do various operations on it (including extracting the data into other formats) with wb_command. Matt Glasser has written some matlab functions that use wb_command -cifti-convert and the matlab gifti toolbox to get the data into matlab, but I don't think we currently have a good way to do spatial operations on it in matlab. I don't know what you mean by "network", and might not be able to help you with it if I did, but others on the list might. Tim On Fri, Jun 6, 2014 at 12:33 PM, Ommen, Jurgen <omme0...@stthomas.edu> wrote: > Hi Tim, > > > > Great, thanks for your fast answer. Generating the dense connectome files > works good. > > > > However, I’m not quite sure about the content of the dense connectome > files. As far as I understood it, it is the complete connectivity matrix on > a voxel-based scale. Is this right? This would be exactly what I need. > > > > My question now would be: Which steps or tools are usually used to extract > the information stored in the dense connectome files for further > post-processing? It would be really great if you could just outline the > steps roughly and the tools I could use to get the network. Is there maybe > a Matlab library available which is able to read .dconn.nii files? > > > > Thanks again for your help, > > Jürgen > > > > *From:* Timothy Coalson [mailto:tsc...@mst.edu] > *Sent:* Wednesday, June 04, 2014 7:42 PM > *To:* Ommen, Jurgen > *Cc:* hcp-users@humanconnectome.org > > *Subject:* Re: [HCP-Users] Brain Connectivity Matrices > > > > I believe we don't include those in the releases, because dense connectome > files are very large (~30GB each). You should be able to generate them by > running wb_command -cifti-correlate on a subject's rfMRI dtseries file. > > > > Tim > > > > > > On Tue, Jun 3, 2014 at 5:55 PM, Ommen, Jurgen <omme0...@stthomas.edu> > wrote: > > Hello everyone, > > > > I’m working on graph theoretic analysis of the human’s brain network. > After studying the documentation of the Q3 release, I’ve only found group > average dense connectome files so far. > > > > I’d like to know if there are any connectivity matrices available for > individual subjects with which I could generate the corresponding > connectome networks. Do you provide this kind of data? Where could I find > it? > > And if not, do you plan to include it in future releases? > > > > > > Thanks for your help in advance and my best regards, > > Jürgen > > > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
