Great, thanks for the fast answer! This helps a lot. Jürgen
From: Timothy Coalson [mailto:[email protected]] Sent: Thursday, July 10, 2014 4:40 PM To: Jennifer Elam Cc: Ommen, Jurgen; [email protected] Subject: Re: [HCP-Users] Map index of dense connectome matrix to name of brain region To expand on the wb_command part, the released versions don't have a friendly way to find that information, but that will be improved somewhat in the next release - the -file-information command will print some information from the XML in cifti files, including parcel names in cifti index order when applicable. In the XML, the parcel names occur in elements like this: <Parcel Name="V1"> and their order in the XML is in CIFTI index order, so you could figure it out that way. We used to call surface vertices "nodes", so some confusion may ensue in our responses if you meant graph nodes (parcels). Tim On Thu, Jul 10, 2014 at 4:27 PM, Jennifer Elam <[email protected]<mailto:[email protected]>> wrote: Hi Jürgen, In the Workbench GUI (wb_view), you can look up surface vertex brainordinates for any loaded surface (e.g. $subject.L.inflated.32k_fs_LR.surf) through the ‘Select Brainordinate’ button in the Information box (turn the Info box on with the “i” button in the upper right of the GUI). When you enter a vertex number for the surface you are interested in, a sphere will appear at that vertex on the appropriate surface in the viewing area and info on position will show up in the Info box. If you have other data files (e.g. a 32k dlabel file) loaded as well, information from that file for that vertex (e.g. a label name) will also appear in the Info box. Using wb_command -nifti-information -print-xml you can get the full CIFTI XML that contains lists of the vertices within each label, which you can parse however you want. Best, Jenn Jennifer Elam, Ph.D. Outreach Coordinator, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387<tel:314-362-9387> [email protected]<mailto:[email protected]> www.humanconnectome.org<http://www.humanconnectome.org> From: [email protected]<mailto:[email protected]> [mailto:[email protected]<mailto:[email protected]>] On Behalf Of Ommen, Jurgen Sent: Thursday, July 10, 2014 3:19 PM To: [email protected]<mailto:[email protected]> Subject: [HCP-Users] Map index of dense connectome matrix to name of brain region Hi, Thanks for the great work on the HCP project. I’m doing some graph analysis on the rs-fMRI dense connectomes. Therefore I’ve created a full and a parcellated dense connectome with the -–cifti-correlation command on a per subject basis using the dlabel file in $subject/MNINonLinear/fsaverage_LR32k/$subject.aparc.a2009s.32k_fs_LR.dlabel.nii. Now I have some results, but in order to verify them I would like to map the indices of this connectome matrix to a brain region name. For example, my parcellated dense connectome is a 148x148 matrix. Where do I find the name of the brain region for the node number 105? Do you provide a txt lookup file for this or is there something similar available? And I’d like to know something similar for the full dense connectome, e.g. in which brain region is the node 45023 located. Is this possible with the HCP workbench and how would I do this? I’m new to the computational neuroscience area, therefore I hope my questions make sense. Thank you very much for your help in advance, Jürgen _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
