Hi Connor, The pipeline has improvements I think you will value -- including providing these 32k surfaces in formats that are more readily usable by wb_command, a utility you might find helpful in other ways. (This is part of workbench.)
Meanwhile, this recent thread shows how to downsample freesurfer_to_fs_LR output: http://brainvis.wustl.edu/pipermail/caret-users/2014-August/006194.html Donna On Aug 15, 2014, at 9:03 AM, Connor Lane <[email protected]> wrote: > Hi Donna, > Yep that's right, I'm looking to resample my own data onto fs_LR. > > You know, I remember seeing freesurfer_to_fs_LR a while ago, but for some > reason I decided it wouldn't work for me. Looking back at it now, it should > work just fine. I think at first I was thrown off that the script didn't also > create 32k resampled surfaces. But I see now that once you have L and R > reg_LR spheres for a subject on their native mesh, you can resample to the > 32k_fs_LR mesh just as you would to the 164k (maybe using wb_command -surface > resample). > > Thank you for the help! I think I'm set for now, I'll be able to complete > what I need to do. I'll keep an eye out for when the HCP pipeline is > released. It sounds exciting, especially the new registration method. > > Thanks again, > Connor > > > On Wed, Aug 13, 2014 at 11:14 AM, Donna Dierker <[email protected]> > wrote: > 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. 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