Hi Joelle and all, we have a pipeline that takes diffusion MRI and T1-weighted data as input and automatically computes structural connectivity matrices for arbitrary cortical parcellations using three different connectivity metrics. It also computes functional connectivity matrices from fMRI data that are in the same space as the structural connectomes (i.e. for the same cortical parcellation). http://www.ncbi.nlm.nih.gov/pubmed/25837600
You can run the pipeline for free on a supercomputer at http://www.nsgportal.org/portal2/tools.action (-> Link: The Virtual Brain Personalized Multimodal Connectome Pipeline) or download it from https://github.com/BrainModes/TVB-empirical-data-pipeline and use it locally (it's however computationally quite heavy so if you haven't access to a supercomputer I would recommend the NSG portal). We didn't test it with HCP data so far, but it shouldn't be a problem. (Contact us in case it doesn't work) All the best, Michael > Hi Jennifer, > > That's good to hear! I don't have much experience with tractography, but > it > looks like bedpostX creates all the files you need for running > probabilistic tractography (probabilistic tractography itself is run with > probtrackX for example). I suppose the probabilistic tractography is > something that would come in a later release. > > Thanks, > Joelle > > > > > On Mon, Nov 23, 2015 at 2:10 PM, Jennifer Elam <[email protected]> > wrote: > >> Hi Joelle and all, >> >> HCP does have running bedpostX on the diffusion data for HCP Subjects on >> our to do list, but this data has not been released yet. We are hoping >> to >> have this available to users by late winter/early spring 2016 after we >> release 7T data. >> >> >> >> 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 >> [email protected] >> www.humanconnectome.org >> >> >> >> *From:* Joelle Zimmermann [mailto:[email protected]] >> *Sent:* Monday, November 23, 2015 12:54 PM >> *To:* Jennifer Elam; [email protected] >> *Subject:* Tractography on diffusion data for SC matrices >> >> >> >> Hi Jennifer, >> >> >> >> I previously posted a question to the mailing list, and wanted to check >> with you as you may have a bit more of an insiders scoop. >> >> >> >> I was wondering whether tractography has been performed on the diffusion >> data for the end of creating structural connectivity matrices for >> individual subjects; or something that is in the plans? I would expect >> this is something that would be of interest to quite a few people, and >> would definitely be of a lot of use to me. >> >> >> >> Thanks, >> >> Joelle >> > > _______________________________________________ > 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
