Re: [HCP-Users] freesurfer directory structure for 32k average

[Harms, Michael]

BTW: There isn't a freesurfer directory corresponding to fsaverage_32k.  Rather, the native freesurfer mesh gets registered to a standardized 164k mesh, which then gets down sampled to a 32k mesh -- see Fig. 16 and the text describing the PostFreeSurfer pipeline in Glasser et al. 2013.  This is all accomplished using various commands in 'wb_command'. cheers, -MH --  Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mha...@wustl.edu From: <Harms>, Michael <mha...@wustl.edu> Date: Thursday, September 4, 2014 9:23 AM To: Satrajit Ghosh <sa...@mit.edu>, "Harms, Michael" <mha...@wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] freesurfer directory structure for 32k average Hi, If you can wait just a little bit longer, you'll be able to see all the exact commands when we release the pipeline scripts, and you won't need to reverse-engineer anything.  I think that would be the most efficient way for you to proceed. cheers, -MH --  Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mha...@wustl.edu From: Satrajit Ghosh <sa...@mit.edu> Date: Thursday, September 4, 2014 9:15 AM To: "Harms, Michael" <mha...@wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] freesurfer directory structure for 32k average hi michael, if i understand correctly these directories contain <subjID>'s data in that fsaverage_LR32k space. (from here i can reverse engineer parts of the fsaverage_32k freesurfer directory structure, but i was specifically wondering if information about fsaverage_32k was available somewhere). let's say i wanted to register my own data to that same fsaverage_32k space, it would be good to have the freesurfer directory corresponding to fsaverage_32k.  i'm assuming at some point in the HCP processing the individual surfaces were registered to this average space and that if done through freesurfer would have required a tif file containing information about the template and the fsaverage_32k directory or a mapping from freesurfer's fsaverage to fsaverage_32k.  cheers, satra On Thu, Sep 4, 2014 at 10:03 AM, Harms, Michael <mha...@wustl.edu> wrote: Hi Satra, Can you be a little more specific about what you are asking for? There are the <subjID>/MNINonLinear/fsaverage_LR32k and <subjID>/T1w/fsaverage_LR32k directories. cheers, -MH --  Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mha...@wustl.edu From: Satrajit Ghosh <sa...@mit.edu> Date: Thursday, September 4, 2014 7:08 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] freesurfer directory structure for 32k average hi folks, is there a freesurfer directory available for the 32k average entity?  i could try to create pieces of such a directory based on the cifti info, but i figured this might actually exist somewhere. cheers, satra _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org 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 HCP-Users@humanconnectome.org 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users