Hi Tianwen, Have you downloaded the 500 Subjects Release Group Average Workbench dataset from the ConnectomeDB splash page? Do that and open Scene 4 (Full) or 5 (Mean gray timeseries-regressed), depending on if you want Full or MGTR fcMRI correlation. This will allow you to load rows of the 468 subject group averaged functional connectivity matrix data from DB without having to download the dense connectivity files.
Do you want to extract group average connectivity maps at specific vertices/subcortical voxels or for many vertices in an ROI? You can manually make ROIs in the Workbench GUI (wb_view) using Border Mode or you can use the .dlabel files provided in the dataset for test ROIs. There are right click options “Show CIFTI Connectivity for Nodes inside Border X” (available by right clicking on a border when an connectivity file is loaded) and “Show CIFTI Connectivity for Parcel ….” (available by right clicking inside a parcel label). These will transfer the matrix row data for every vertex within a border or parcel, and then display the averaged connectivity across the parcel. Use this with caution because it takes a long time to retrieve many (hundreds or thousands) matrix rows to show the average. I would stick with small ROIs for starters. You can save the connectivity map you display either by IDing individual vertices/voxels or by the averaging across an ROI/parcel: Go to the Connectivity tab and click the Copy button to the left of the listed Connectivity File link. This creates a *.dscalar file with the particular connectivity map you are displaying. These files should show up in the Layer tab File dropdowns in the Overlay Toolbox. You can save the files you create with File menu > Save/Manage Files before quitting Workbench, for later use. Hope this answers your question. Let me know how it goes if you give it a try. 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 <tel:314-362-9387> 314-362-9387 <mailto:[email protected]> [email protected] <http://www.humanconnectome.org> www.humanconnectome.org From: [email protected] [mailto:[email protected]] On Behalf Of Tianwen Chen Sent: Tuesday, August 05, 2014 11:19 PM To: [email protected] Subject: [HCP-Users] using workbench to extract ROI timesries Hi HCP users, Is it possible to extract averaged ROI timeseries using workbench without downloading subject rsfMRI data? Thanks, Tianwen _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
