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

[Glasser, Matthew]

164k also does not exist in FreeSurfer formats so you would have to write your own conversion back. From: Satrajit Ghosh <sa...@mit.edu> Date: Thursday, September 4, 2014 at 10:14 AM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "Marcus, Dan" <dmar...@wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] freesurfer directory structure for 32k average thank you matt and michael, the 164k surface is fine. as long as something is there that allows us to register our data to the average space, at least most of my present needs would be met. also, as anderson noted, we all have various tools that work with the freesurfer directory structures and formats. while other tools are being adapted/extended to NIFTI/GIFTI/CIFTI both for data conversion and visualization, it will let us continue to use our existing tools on the average surface. cheers, satra On Thu, Sep 4, 2014 at 11:01 AM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: It’s worth noting that the 32k data is never in FreeSurfer formats, only the native mesh data is in FreeSurfer format.  Also, the FreeSurfer data does not necessarily align with any of the other data we are releasing (it is in it’s own strange 1mm volume space).  Thus, I don’t plan to provide support use of the FreeSurfer formatted data (nor will the Connectome Workbench tools which only read NIFTI/GIFTI/CIFTI) at all and don’t recommend anyone uses it.   Peace, Matt. From: Satrajit Ghosh <sa...@mit.edu> Date: Thursday, September 4, 2014 at 9:54 AM To: "Marcus, Dan" <dmar...@wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] freesurfer directory structure for 32k average thanks dan! cheers, satra On Thu, Sep 4, 2014 at 10:48 AM, Marcus, Dan <dmar...@wustl.edu> wrote: Anderson, Satra, We are planning to distribute the Freesurfer directories as a patch to the current release and to include them in future releases.  I'm not sure of the exact timeline for the patch, but I'd think sometime in the coming weeks. -Dan From: "Anderson M. Winkler" <wink...@fmrib.ox.ac.uk> Date: Thursday, September 4, 2014 9:26 AM Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] freesurfer directory structure for 32k average Hi Michael, I'd second Satra's request: it'd be great to have the original FS directory structure available somewhere -- many of us have scripts that expect that file structure, and also those same file formats that are very easy to read. Thanks! All the best, Anderson On 4 September 2014 15:23, Harms, Michael <mha...@wustl.edu> wrote: 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. 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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.   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