Thanks Donna, much obliged.
> On Oct 12, 2016, at 5:09 PM, Dierker, Donna <do...@wustl.edu> wrote: > > Search for MSMSulc here: > > https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh > > <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 > > <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> >> 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> 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> 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> on behalf of Jared P >>>> Zimmerman <jar...@mail.med.upenn.edu> >>>> Date: Tuesday, October 11, 2016 at 3:12 PM >>>> To: Timothy Coalson <tsc...@mst.edu> >>>> Cc: "hcp-users@humanconnectome.org" <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> 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> 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 >>>>>> www.humanconnectome.org >>>>>> >>>>>> >>>>>> From:hcp-users-boun...@humanconnectome.org >>>>>> <hcp-users-boun...@humanconnectome.org> on behalf of Peter McColgan >>>>>> <pmccolga...@qub.ac.uk> >>>>>> Sent: Tuesday, October 4, 2016 9:29:30 AM >>>>>> To: 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 >>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>>>> _______________________________________________ >>>>>> HCP-Users mailing list >>>>>> HCP-Users@humanconnectome.org >>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>>> >>>>> _______________________________________________ >>>>> HCP-Users mailing list >>>>> HCP-Users@humanconnectome.org >>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> >>>> _______________________________________________ >>>> HCP-Users mailing list >>>> 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 >>> >>> >>> ________________________________ >>> 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 http://lists.humanconnectome.org/mailman/listinfo/hcp-users
