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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