You just go to file menu open file and change to different file types. Peace,
Matt. From: Osama Abdullah <osama.abdul...@utah.edu<mailto:osama.abdul...@utah.edu>> Date: Thursday, April 6, 2017 at 8:34 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] hcp_fix and correlation maps Exactly Matt, in principal what you explained below is what we need. The wb_view only accepts spec or scene files (unless I am misunderstanding) and not sure how to build or properly add dyconn layer, dtseries, projecting onto cortical and subcritical ROI layers or grayordinates. We are still novice with the wb_view functionality so excuse us. Best. Osama Sent from my mobile phone On Apr 6, 2017, at 5:58 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: If you want to explore the functional connectivity, you can do that by loading the dtseries into Connectome Workbench and selecting the dyconn layer and clicking on the surface or in the subcortical grey matter in the volume. Is this what you are after or something else? Peace, Matt. From: Osama Abdullah <osama.abdul...@utah.edu<mailto:osama.abdul...@utah.edu>> Date: Wednesday, April 5, 2017 at 5:54 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] hcp_fix and correlation maps Thanks Matt. Yes, fix.log showed the error location and after correcting it we now can get the "cleaned" series (dense and atlas). What do you recommend the best way for us to display the connectivity map (after running wb_command correlation) for single patient and using different seeding locations. It's preferred to have dynamic seed placement that yields specific connectivity pattern to that specific seed. All the best. Osama ________________________________ From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Wednesday, April 05, 2017 1:52 PM To: Osama Abdullah; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] hcp_fix and correlation maps Unfortunately not all of the errors of ICA+FIX are reported to the main stderr. You’ll need to look in the log files inside the directory created by ICA+FIX to see what the error was (in matlab or R). There isn’t usually any need to add additional files to the spec file (this simply causes them to be opened when you open the spec file). Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Osama Abdullah <osama.abdul...@utah.edu<mailto:osama.abdul...@utah.edu>> Date: Wednesday, April 5, 2017 at 2:43 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] hcp_fix and correlation maps Dear HCP Experts, We are applying the hcp_fix pipeline on Prisma-acquired data (according to the Life Span protocol) and it completed without errors (although it took significant effort on installing the proper R packages). Nonetheless, we cannot find the resulting files that are labelled "clean" anywhere despite the lack of errors. The closest time series we see are the rfMRI_REST1_PA_hp2000.nii and rfMRI_REST1_PA_Atlas.dtseries.nii. Are those overwritten to reflect the results after completing the whole hcp_fix procedure? Second question, say we get the cleaned time series, and we use the wb_command to generate the Correlation (connectivity) maps, how can we add the time series and connectivity maps to the existing "spec" files (for example subjectIDr.32k_fs_LR.wb) so that we can evaluate myelin maps along the connectivity maps? We used the wb_command -add-to-spec-file option but the correlation maps didn't show any intensities on wb_view. Thanks. Osama Osama Abdullah, PhD Department of Neurology School of Medicine University of Utah 36 S. Wasatch Drive Salt Lake City, UT 84112 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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