We do need to get an MSM binary out with a revised MSMSulc config file. This will hopefully happen soon, we are just waiting for the author of a software library to e-mail us back about some licensing stuff.
Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Jared P Zimmerman <jar...@mail.med.upenn.edu<mailto:jar...@mail.med.upenn.edu>> Date: Wednesday, October 12, 2016 at 4:36 PM To: "Dierker, Donna" <do...@wustl.edu<mailto:do...@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] Glasser nature atlas Thanks Donna, much obliged. On Oct 12, 2016, at 5:09 PM, Dierker, Donna <do...@wustl.edu<mailto:do...@wustl.edu>> wrote: Search for MSMSulc here: https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh *refsulc* get copied to subject dir from here: https://github.com/Washington-University/Pipelines/tree/7cc0bf1863cbc8a1a7ab9c6dd48a25de9be9bae7/global/templates/standard_mesh_atlases On Oct 12, 2016, at 10:53 AM, Jared P Zimmerman <jar...@mail.med.upenn.edu<mailto:jar...@mail.med.upenn.edu>> wrote: Thanks Michael, Donna, and Matt, RE: Michael, definitely aware this is an inferior approach to true subject-specific parcellation but given that we don’t have the requisite data to run the classifier this seems like an appropriate approach to use the parcellation. RE: Donna and Matt, thanks for the advice, I think using an MSM sulc approach is something we will definitely want to look into, but looking over the git repo quickly I don’t see an MSM sulc script. There’s the MSM all pipeline, but that seems like it can only use myelin maps, RSNs or topography and doesn’t have an option for sulcal depth. Where might I find an MSM algorithm that can use sulcal depth maps to register? Thanks, Jared On Oct 12, 2016, at 9:48 AM, Dierker, Donna <do...@wustl.edu<mailto:do...@wustl.edu>> wrote: If you can’t do MSMAll, then consider using just sulc, rather than sulc+curv. See figure 4, row B, in Emma Robinson’s paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4190319/figure/F4/ I have heard David describe curvature as capturing more local folding, sulc global folding. In my experience, curvature varies too much across subjects, while sulc seems a more reasonable driver for intersubject registration. For intrasubject registration across timepoints, however, curvature is your friend. On Oct 11, 2016, at 6:54 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Using folding-based alignment won’t be as good as areal-feature-based alignment, but I wouldn’t worry about the alignment being any worse than any other comparison of two studies driven by folding-based alignment. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Jared P Zimmerman <jar...@mail.med.upenn.edu<mailto:jar...@mail.med.upenn.edu>> Date: Tuesday, October 11, 2016 at 3:12 PM To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Glasser nature atlas I have a related question to this. I’d like to use the parcellation on some more traditional volume data (i.e. 3x3x3mm voxels, 3s TR). I have made fs_LR surfaces from free surfer using the wb_command shortcuts for it, as in here: https://wiki.humanconnectome.org/download/attachments/63078513/Resampling-FreeSurfer-HCP.pdf?version=1&modificationDate=1472225460934&api=v2 but I am missing the registration from subject surface to group average. Is this registration, or the validity of the parcellation, dependent on MSMAll or would an MSMSulc registration be effective (enough) here? The paper and parcellation are clearly based on MSMAll and this was essential in generating parcellation, but since I don’t have the requisite rest data to do an MSMAll register, would an MSMSulc registration be sufficient for ultimately translating back to the subject volume? I read the above discussion about a month ago and didn’t see this covered, but I don’t know if that was addressed in the discussion since. Tanks, Jared On Oct 4, 2016, at 5:45 PM, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote: Making a "nifti version" isn't a simple conversion, as some lengthy conversations on this list have elaborated on. The good news: if you want a single-subject-specific version, that is possible, using -cifti-separate and -label-to-volume-mapping, using the subject's own surfaces. The bad news: if you want it to be a group atlas, the currently popular volume registration methods aren't good enough at cortical area alignment to make our parcellation meaningful in a group-average volume space, and thus we do not recommend making a volumetric version in such a space. In the meantime, surface registration avoids several difficulties inherent to volume registration, and was instrumental in being able to create the parcellation at all (via alignment of areal features). For more detailed discussion: https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03078.html Tim On Tue, Oct 4, 2016 at 9:47 AM, Elam, Jennifer <e...@wustl.edu<mailto:e...@wustl.edu>> wrote: Hi Peter, The data for the new parcellation are available in the BALSA database, see this thread: http://www.mail-archive.com/hcp-users@humanconnectome.org/msg02876.html We recommend using the included Connectome Workbench scene file to conveniently view the data in the wb_view part of the software platform. Get Connectome Workbench here: https://www.humanconnectome.org/software/get-connectome-workbench.html Many of the files are in the CIFTI data format, which has a lot of advantages, but if you need NIFTI versions, you can use wb_command (distributed as part of Connectome Workbench) to do the conversion. There's lots of help for using wb_command in the HCP-Users mail archive, and/or you could post more questions to the list. Best, Jenn Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 e...@wustl.edu<mailto:e...@wustl.edu> www.humanconnectome.org From:hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Peter McColgan <pmccolga...@qub.ac.uk<mailto:pmccolga...@qub.ac.uk>> Sent: Tuesday, October 4, 2016 9:29:30 AM To: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: [HCP-Users] Glasser nature atlas Dear HCP team, Is it possible to download a nifti version of the Glasser atlas featured recently in nature? Thanks bw Peter _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ 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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ 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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ 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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
