Hi Tim, Thanks for your reply. I see my mistake was in assuming the output from cifti-separate would be 32k x 32k and loading it in to matlab as such, using *fread(fid,[32492 32492], 'float32')*. Since the file is actually 32k x 91k it's no wonder the vertices aren't correct.
Is it possible to get to the 32k x 32k matrices using -cifti-restrict-dense-map (instead of 29k x 29k) and if so, can you advise how? Can I simply use a surf.gii file as -left-roi and -right-roi? Presumably I can follow this with -cifti-convert -to-gifti-ext to convert from dconn to metric and then load the matrix into matlab using fread as before? Thanks again! Estrid On Mon, Mar 13, 2017 at 7:51 PM, Timothy Coalson <[email protected]> wrote: > That command should do what you intended, though it will give you two 32k > x 91k files, not 32k x 32k. Another possibility for doing this (which can > also get you to the single-hemisphere 29k x 29k cifti file by running it > twice) is -cifti-restrict-dense-map, which is also far less painful to load > the results into wb_view, as it remains a dconn file (data loaded on > demand, not in advance, knows not to show it as 91k maps in a combobox). > > I ran the exact command you quoted on the same file downloaded from > ConnectomeDB, using workbench v1.1.1 linux64 (debian/ubuntu) as previously > released on our website, and the resulting files I got look nothing like > your capture (I am trying it again with v1.2.3 now, but it takes a while to > run things on files this large - very little has changed in this command, > so I expect the same result). Did you do anything after the > -cifti-separate that you didn't mention? Which map(s) in the output file > did you check? What version of workbench and OS did you run it on, and how > much memory did the machine have? > > Tim > > > On Mon, Mar 13, 2017 at 10:13 AM, Estrid Jakobsen <[email protected]> > wrote: > >> Hi folks, >> >> I have a question regarding extracting the left and right hemispheres >> from .dconn cifti files. I've tried using wb_command -cifti-separate on the >> 820-subject group average dense connectome (see command below), but when I >> then visualize a connectivity vector from the resulting 32k x 32k matrix, >> the vertices appear to be scrambled (see attached image). I'm guessing this >> might have something to do with the command not being intended for >> separating symmetrical matrices and perhaps only extracting correctly along >> one dimension...? >> >> Is there a way to extract the left and right 32k matrices from the dense >> connectome, or would I have to go back and create them myself from the PCA >> Eigenmaps? >> >> Thanks in advance! >> >> Estrid >> >> wb_command -cifti-separate >> HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii >> ROW -metric CORTEX_RIGHT HCP_S900_820_rfMRI_MSMAll_grou >> pPCA_d4500ROW_zcorr_RIGHT.func.gii -metric CORTEX_LEFT >> HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr_LEFT.func.gii >> >> >> **************** >> Estrid Jakobsen >> >> Postdoctoral Fellow >> Cognitive Neurosciences >> Montreal Neurological Institute and Hospital, McGill University >> >> Max Planck Research Group Neuroanatomy and Connectivity >> Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > -- **************** Estrid Jakobsen Postdoctoral Fellow Cognitive Neurosciences Montreal Neurological Institute and Hospital, McGill University Max Planck Research Group Neuroanatomy and Connectivity Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
