I think Eran is just looking for the regional statistics, so downloading the whole package is a bit extreme and would still require some shenanigans to extract the stats (though it's the best option for anyone wanting the full FS directory tree). Eran, I think we can add the additional regional metrics (curvature, etc) to a downloadable spreadsheet. There's also some XNAT wizardry that can be done to pull these data via REST services. Give us a few days, and we should be able get these data for you in a user friendly format.
-D From: 'Jennifer Elam' <[email protected]<mailto:[email protected]>> Date: Friday, December 19, 2014 3:14 PM To: "'Dayan, Eran (NIH/NINDS) [F]'" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Accessing Freesurfer measurements via ConnectomeDB Hi Eran, Several volume measures are available in the FreeSurfer summary statistics available in the filters you found on the Subject Dashboard. However, for all the information that you want, download the “Structural Extended Preprocessed” package from the Download Packages page with the MRI and Preprocessed filters selected. This package has all the intermediate FreeSurfer pipeline outputs in it and is 611GB for all 526 subjects with structural MRI data in the current release. 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]] On Behalf Of Dayan, Eran (NIH/NINDS) [F] Sent: Friday, December 19, 2014 2:47 PM To: [email protected]<mailto:[email protected]> Subject: [HCP-Users] Accessing Freesurfer measurements via ConnectomeDB I am trying to access volumetric data generated by the Freesurfer pipeline for the entire s500 release. In ConnectomeDB it’s very easy to access subcortical volumes and cortical (surface) area and thickness measurements, as these are included in the CSV file provided for the entire dataset (and can also be easily accessed with a simple combination of filters). I was wondering, though, if there’s an easy way to download, at once, other surface measurements, like volume or mean curvature ? I could only access these measurements, on a subject by subject basis, by going to each subject’s “Freesurfer Results” section. Is there a combination of filters that I may have missed that would allow me to download all this data at once? Many thanks Eran _______________________________________________ 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
