Great thanks for your helpful reply. Unfortunately I'm not working with the HCP data exclusively. In addition we have our own data which has been pre-processed with the standard FreeSurfer -recon-all pipeline. Thus these subjects do not have a 32k or 164k mesh, instead they have typical output surfaces from FreeSurfer...
So if I understand correctly I could do the following: * Use the '"freesurfer_to_fs_LR" script to create 32k and/or 164k mesh surfaces for each subject * The Gordon parcellation would then have a direct correspondence with these meshes (no resampling required) * The FreeSurfer "mri_label2vol" tool could then be used to create subject specific parcellation maps Is this correct? Am I missing something? Thanks, David -----Message d'origine----- De : Donna Dierker [mailto:[email protected]] Envoyé : 08 March 2016 18:05 À : Slater David Objet : Re: [HCP-Users] Cortical parcellations in Connectome Workbench and FreeSurfer I hope someone who has actually done something like this answers, but this page might be helpful: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_label2vol I'm less familiar with Freesurfer tools, but conceptually: * The Gordon parcellation is available on 32k mesh (or 164k at least). * The subject's individual surface is available in both of those meshes. * The parcellation could be projected to the ribbon between the white and pial surfaces (possibly via mri_label2vol). * It would not be necessary to resample the parcellation onto the native mesh to do this. * The subject's native mesh is also available in one of the HCP-downloadable packages. * There is a way, using -surface-project-unproject, to convert stuff back to native mesh, but it's tough to get your head around it, and I'm not sure it's the shortest path in this case. Again, hopefully someone who has done this will reply. :) On Mar 8, 2016, at 4:14 AM, Slater David <[email protected]> wrote: > Hi, > > I have a parcellation I would like to work with from the following paper: > > Gordon, E.M., Laumann, T.O., Adeyemo, B., Huckins, J.F., Kelley, W.M., > Petersen, S.E., 2014. Generation and Evaluation of a Cortical Area > Parcellation from Resting-State Correlations. Cereb. Cortex bhu239-. > > > The cortical parcellations are saved in .gii format for both the fs_LR 32k > and 164k meshes. My aim is to create a parcellated volume image for each of > my subjects in their native space. I know how to do this with Freesurfer > tools but I am a little lost with the fs_LR 32k and 164k mesh formats. > > If I had the parcellation in a standard Freesurfer subject space (e.g. > fsaverage) I would transform the parcalletion to the subject native space and > convert the surface labels to a volume parcellation. This is similar to how > the aparc niftii files are generated. > > How can I get a parcellation of the fs_LR 32k or 164k meshes into a subject's > native space parcellation? Or alternatively, how can I convert fs_LR 32k or > 164k vertex values to the fsaverage surface? > > Thanks, > David > _______________________________________________ > 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
