Hi Satra, In wb_command, we now use a different resampling strategy from the Caret-based deformation maps described in the URL you mentioned.
See, for example, http://www.mail-archive.com/hcp-users%40humanconnectome.org/msg00569.html and related hcp-users postings. This will also be evident in the HCP pipeline scripts once these are released. David On Sep 4, 2014, at 10:30 AM, Satrajit Ghosh <[email protected]> wrote: > thanks matt. > > i just found this page: > http://brainvis.wustl.edu/wiki/index.php//Caret:Atlases/Conte69_Atlas > > looks like most details i need are there. but i suspect some of the caret > commands are now available within the workbench as well. > > cheers, > > satra > > > On Thu, Sep 4, 2014 at 11:19 AM, Glasser, Matthew <[email protected]> > wrote: > 164k also does not exist in FreeSurfer formats so you would have to write > your own conversion back. > > From: Satrajit Ghosh <[email protected]> > Date: Thursday, September 4, 2014 at 10:14 AM > To: Matt Glasser <[email protected]> > Cc: "Marcus, Dan" <[email protected]>, "[email protected]" > <[email protected]> > > 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 <[email protected]> > 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 <[email protected]> > Date: Thursday, September 4, 2014 at 9:54 AM > To: "Marcus, Dan" <[email protected]> > > Cc: "[email protected]" <[email protected]> > 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 <[email protected]> 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" <[email protected]> > Date: Thursday, September 4, 2014 9:26 AM > > Cc: "[email protected]" <[email protected]> > 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 <[email protected]> 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: [email protected] > > From: Satrajit Ghosh <[email protected]> > Date: Thursday, September 4, 2014 9:15 AM > To: "Harms, Michael" <[email protected]> > Cc: "[email protected]" <[email protected]> > 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 <[email protected]> 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: [email protected] > > From: Satrajit Ghosh <[email protected]> > Date: Thursday, September 4, 2014 7:08 AM > To: "[email protected]" <[email protected]> > 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 > [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. 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