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 <[email protected]> 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/[email protected]/msg03078.html > <https://www.mail-archive.com/[email protected]/msg03078.html> > > Tim > > > On Tue, Oct 4, 2016 at 9:47 AM, Elam, Jennifer <[email protected] > <mailto:[email protected]>> wrote: > Hi Peter, > > The data for the new parcellation are available in the BALSA database, see > this thread: > http://www.mail-archive.com/[email protected]/msg02876.html > <http://www.mail-archive.com/[email protected]/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 > <https://www.humanconnectome.org/software/get-connectome-workbench.html> > > Many of the files are in the CIFTI data format > <http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-help>, > which has a lot of advantages, but if you need NIFTI versions, you can use > wb_command <http://www.humanconnectome.org/software/workbench-command.php> > (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 <tel:314-362-9387> > [email protected] <mailto:[email protected]> > www.humanconnectome.org <http://www.humanconnectome.org/> > > From: [email protected] > <mailto:[email protected]> > <[email protected] > <mailto:[email protected]>> on behalf of Peter McColgan > <[email protected] <mailto:[email protected]>> > Sent: Tuesday, October 4, 2016 9:29:30 AM > To: [email protected] <mailto:[email protected]> > 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 > [email protected] <mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <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 > <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> > _______________________________________________ > 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
