Thanks Tim! I will consider your suggestions. Reza
On Thu, Oct 25, 2018 at 11:51 PM Timothy Coalson <tsc...@mst.edu> wrote: > If you have their cifti indices then you can just make a new cifti dscalar > with only those grayordinates set to 1 (double check this in wb_view, > matlab uses 1-based indexing, and I don't remember which convention we use > for cifti indices). If you don't have the cifti indices, you can use > -cifti-export-dense-mapping output to make text files that translate > between them and vertex/voxel. I suggest loading some standard dscalar > file to use as the template for saving the data out (use > ciftiopen/ciftisavereset, the ft_read_cifti and related functions do some > unexpected things with the cifti matrix). > > Single points out of a dconn are likely to be noisy, you may also want to > consider -cifti-parcellate (if possible, -cifti-parcellate on the dtseries, > and then do the correlations on the parcellated timeseries, rather than > averaging correlations together). > > Tim > > > On Thu, Oct 25, 2018 at 10:20 AM, Reza Rajimehr <rajim...@gmail.com> > wrote: > >> Thanks Matt! Looks like -cifti-restrict-dense-map can do what I want if I >> run it twice (first run it along the COLUMN direction to get an output, >> then run it again on the output along the ROW direction). For this to work, >> I need to specify an roi file. In a .mat file, I have a list of >> grayordinate vertices/voxels (some in left hemi, some in right hemi, some >> in subcortex). How can I put all of them in one cifti roi file in Matlab? >> >> Reza >> >> >> On Thu, Oct 25, 2018 at 2:40 PM Glasser, Matthew <glass...@wustl.edu> >> wrote: >> >>> Yes that would be a better solution. I think the wb_command >>> -cifti-restrict-dense-map might work. >>> >>> Matt. >>> >>> From: Reza Rajimehr <rajim...@gmail.com> >>> Date: Thursday, October 25, 2018 at 3:16 AM >>> To: Matt Glasser <glass...@wustl.edu> >>> Cc: Timothy Coalson <tsc...@mst.edu>, "hcp-users@humanconnectome.org" < >>> hcp-users@humanconnectome.org> >>> >>> Subject: Re: [HCP-Users] Question about dense functional connectome >>> >>> We tried to open *.dconn.nii in Matlab using ft_read_cifti on an Ubuntu >>> system with 48 GB RAM. It used 48 GB RAM and 18 GB (out of 60 GB) swap, >>> then Matlab gave out of memory error! Will try to use a system with even >>> higher RAM. >>> >>> Tim: We have a list of 913 grayordinate voxels (we have their voxel >>> numbers/indices). These voxels are somewhat distributed in gray matter. We >>> are basically interested in the functional connectivity matrix just for >>> these 913 voxels (i.e. a 913 * 913 matrix). Is it possible to use >>> wb_command to select part of *.dconn.nii corresponding to the voxels of >>> interest? >>> >>> Best, >>> Reza >>> >>> >>> On Thu, Oct 25, 2018 at 3:49 AM Glasser, Matthew <glass...@wustl.edu> >>> wrote: >>> >>>> Use swap space. >>>> >>>> Matt. >>>> >>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Timothy >>>> Coalson <tsc...@mst.edu> >>>> Date: Wednesday, October 24, 2018 at 4:57 PM >>>> To: Reza Rajimehr <rajim...@gmail.com> >>>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>>> Subject: Re: [HCP-Users] Question about dense functional connectome >>>> >>>> The cifti format doesn't support that, because it is designed to allow >>>> use without loading the entire file into memory - there is no obvious file >>>> organization that would allow efficient loading of a full row from a single >>>> triangular file, when seek times are nontrivial (rotating disks). I don't >>>> believe we have these files in any other format. I'm also not sure how >>>> easy it would be to work on such a matrix in matlab. If wb_command is >>>> capable of doing the operations you want, it is usually possible for it to >>>> do them without loading the entire cifti file into memory at once. wb_view >>>> will also display maps from it without loading the entire file into memory. >>>> >>>> DDR4 has 16GB modules available at reasonable prices, which should >>>> allow recent computers with even 4 slots for memory to expand to 64GB. You >>>> should also consider the "high-end desktop" platforms (threadripper, >>>> lga2066, lga2011), which typically offer 8 memory slots, and processors >>>> with more cores. >>>> >>>> Tim >>>> >>>> >>>> On Wed, Oct 24, 2018 at 3:56 PM, Reza Rajimehr <rajim...@gmail.com> >>>> wrote: >>>> >>>>> Hi, >>>>> >>>>> We are trying to unzip and load dense functional connectome >>>>> (HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.zip or >>>>> HCP_S900_820_rfMRI_MSMSulc_groupPCA_d4500ROW_zcorr.zip from >>>>> >>>>> https://www.humanconnectome.org/study/hcp-young-adult/article/announcing-release-of-s900-ptn-and-other-group-average-data) >>>>> in Matlab on a system that has 32 GB RAM. This is of course impossible due >>>>> to the fact that the files are ~33 GB in size. Due to matrix symmetry, it >>>>> would be sufficient to store only the upper or lower triangular part of a >>>>> functional connectivity matrix, reducing memory occupancy by about 50% >>>>> (Loewe et al., 2016). Does HCP provide such files that could be >>>>> memory-friendly? >>>>> >>>>> Best, >>>>> Reza >>>>> >>>>> _______________________________________________ >>>>> HCP-Users mailing list >>>>> HCP-Users@humanconnectome.org >>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>>> >>>> >>>> _______________________________________________ >>>> 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. 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. 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