[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-

[HCP-Users] Problem running the HCP DTI data in a high performance cluster

Dear HCP experts, We've been having difficulties with running BEDPOSTX on the cluster and we do not know what the problem is, so if anybody would have any suggestions, we would be very grateful. The problem is the following. When running the following command on the clusters with FSL 5.6 bedpo

Re: [HCP-Users] Problem running the HCP DTI data in a high performance cluster

Hi Nele Do you run that in parallel or on a single node? In any case you need enough memory to be able to process HCP data. Bedpostx calls fsl_sub to send jobs to the cluster queue. If your cluster’s default memory allocation limits are low, you can easily run out of memory. You could slightly

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

Hi Satra, Can you be a little more specific about what you are asking for? There are the /MNINonLinear/fsaverage_LR32k and /T1w/fsaverage_LR32k directories. cheers, -MH --  Michael Harms, Ph.D. --- Conte Center for the Neuroscienc

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

hi michael, if i understand correctly these directories contain '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 s

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. -

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,

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

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" mailto:wink...@fm

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

Hi Dan, Sounds great! Thanks! Anderson On 4 September 2014 15:48, Marcus, Dan 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

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

thanks dan! cheers, satra On Thu, Sep 4, 2014 at 10:48 AM, Marcus, Dan 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

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

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.  Thi

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

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 s

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 f

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

164k also does not exist in FreeSurfer formats so you would have to write your own conversion back. From: Satrajit Ghosh Date: Thursday, September 4, 2014 at 10:14 AM To: Matt Glasser Cc: "Marcus, Dan" , "hcp-users@humanconnectome.

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

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,

Re: [HCP-Users] Timings of the task fMRI data

Hi Ryota, Please see my comments inline below. I hope the additional info helps! --Greg Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiolo

Re: [HCP-Users] Timings of the task fMRI data

Dear Greg, Thank you very much for your clarification! Best, Ryota On Thu, Sep 4, 2014 at 6:42 PM, Greg Burgess wrote: > Hi Ryota, > > Please see my comments inline below. I hope the additional info helps! > > --Greg > > > Gr

[HCP-Users] test

Sorry, this is just a test. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

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

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