hi david, thank you for the pointer. i'll read the newer strategy.
cheers, satra On Thu, Sep 4, 2014 at 10:28 PM, David Van Essen <[email protected]> wrote: > 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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