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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