Connor has acquired his own data, so he needs something like the soon-to-be-released Human Connectome Project (HCP) pipeline (ideally) or freesurfer_to_fs_LR, if I understand his message correctly. The pipeline uses MSM, a surface-based registration program that will also be released soon. (And the HCP is using a pre-release version of it.) There is a paper contrasting the registration methods here:
https://www.researchgate.net/publication/263475767_Correspondences_between_retinotopic_areas_and_myelin_maps_in_human_visual_cortex I'm not sure what the timetable for releasing the HCP pipeline is. How soon do you need this, Connor? On Aug 13, 2014, at 12:42 AM, "Glasser, Matthew" <[email protected]> wrote: > fs_LR is not in fsaverage space it is fs_LR space. But I do think the > spheres are what you are looking for. I think your command is fine though we > usually put all of the surfaces of a given mesh and volume space in their own > folder and don’t including stuff like resampled_. > > Peace, > > Matt. > > From: Connor Lane <[email protected]> > Date: Tuesday, August 12, 2014 at 7:07 PM > To: "Elam, Jennifer" <[email protected]> > Cc: "[email protected]" <[email protected]> > Subject: Re: [HCP-Users] fs_LR spheres in fsaverage space > > Hi Jenn, > > Thank you for the quick reply. But I don't think those spheres are in > fsaverage space, are they? Basically, I have some structural images that I've > collected and analyzed with freesurfer. And now I want to resample the native > surfaces I've got onto the 164k_fs_LR and 32k_fs_LR meshes so that vertex N > is in the same anatomical location in each hemisphere. I was thinking if I > could find spheres of these meshes in left and right hemisphere fsaverage > space. I could run something like this to get what I need: > > wb_command -surface-resample `my subject's left pial` `my subject's left > sphere.reg` `left 164k_fs_LR sphere in fsaverage space` BARYCENTRIC > L.resampled_pial.164k_fs_LR.surf.gii > > What do you think, is this the right way to go about it? > > Thanks, > Connor > > > On Mon, Aug 11, 2014 at 9:57 AM, Jennifer Elam <[email protected]> wrote: >> Hi Connor, >> >> In the preprocessed data, look in the SubjectID/MNINonLinear directory for >> the 164k_fs_LR sphere surfaces and the >> SubjectID/MNINonLinear/fsaverage_LR32k directory for the 32k_fs_LR sphere >> surfaces. >> >> For future reference, all the files being distributed in all the >> downloadable HCP packages/Connectome In a Box are listed in 500 Subjects >> Reference Manual Appendix III. >> >> 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:[email protected] >> [mailto:[email protected]] On Behalf Of Connor Lane >> Sent: Monday, August 11, 2014 12:50 AM >> To: [email protected] >> Subject: [HCP-Users] fs_LR spheres in fsaverage space >> >> Hello HCP users, >> >> Are there 164k and 32k fs_LR sphere files that are in fsaverage lh and rh >> spaces somewhere? I'm looking for them so I can resample native surfaces >> onto the fs_LR meshes using wb_command -surface-resample. >> >> Thank you in advance, >> Connor >> _______________________________________________ >> 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 > > > 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 > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
