Hi Georgios, Looks like you asked for adaptive barycentric resampling without providing areas to use (the algorithm does not accept spherical surfaces to be the source of anatomical vertex areas). Resampling a dense connectome would only be appropriate for tractography data. For fMRI data, you want to average the timeseries prior to running functional connectivity at the lower resolution.
Peace, Matt. On 7/16/16, 9:59 AM, "Georgios Michalareas" <giorgos.michalar...@esi-frankfurt.de> wrote: >Thanks for the tip Matt. > >I ll stick to parcellations for comparing fMRI and MEG connectivity in >the practicals. > >But in any case , if one would want to do such a deconn resampling , do >you know what is the mistake(s) I am doing in the command below? > >Thanks again > >Giorgos > > >On 7/16/2016 4:49 PM, Glasser, Matthew wrote: >> Hi Georgios, >> >> I would not recommend downsampling a dense connectome. Instead it would >> be better to downsample the dense timeseries and then recompute the >>dense >> connectome. >> >> Peace, >> >> Matt. >> >> On 7/16/16, 9:47 AM, "hcp-users-boun...@humanconnectome.org on behalf of >> Georgios Michalareas" <hcp-users-boun...@humanconnectome.org on behalf >>of >> giorgos.michalar...@esi-frankfurt.de> wrote: >> >>> Hi everyone, >>> >>> i am trying for the MEG practicals to downsample a 32K dconn fMRI group >>> functional connectivity cifti: >>> >>> HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii >>> >>> into a dconn cifti in the 4K space that we use in the MEG analysis in >>>OT4. >>> >>> I am trying to use cifti-resample to do so. I know i have to use it >>> twice, once along COLUMN and then along ROW directions. >>> >>> However I am not sure how to set the cifti-resample input arguments >>> correctly. >>> >>> >>> I have the following files : >>> >>> Input functional connectivity file from fMRI in 32K space: >>> HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii >>> >>> Input Sphere Left (32K space): S900.L.sphere.32k_fs_LR.surf.gii >>> >>> Input Sphere Right (32K space): S900.R.sphere.32k_fs_LR.surf.gii >>> >>> Output Sphere Left (4K space): Sphere.4k.L.surf.gii >>> >>> Output Sphere Right (4K space): Sphere.4k.R.surf.gii >>> >>> I have a "template" (not sure if it is actually suitable for a >>>template) >>> dconn file in the 4K space, called testtemplate4K.dconn.nii. This is a >>> just a dconn file of functional connectivity computed directly from MEG >>> data in the 4K space. >>> >>> The issue is that the 32K functional connectivity matrix contains >>> connectivity between all vertices , in both left and right hemispheres >>> and i am not sure if such a connectivity file can be divided into left >>> and right. So this file is defined over both hemispheres. >>> >>> Then I have the input and output spaces defined with sphere files, >>> different for left and right hemispheres. >>> >>> After reading the description of cifti-resample I tried running the >>> following (with wb_command 1.2): >>> >>> wb_command -cifti-resample >>> HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii COLUMN >>> testtemplate4K.dconn.nii COLUMN ADAP_BARY_AREA CUBIC >>> testdconnresamp1.dconn.gii -left-spheres >>> S900.L.sphere.32k_fs_LR.surf.gii Sphere.4k.L.surf.gii -right-spheres >>> S900.R.sphere.32k_fs_LR.surf.gii Sphere.4k.R.surf.gii >>> >>> and i got the error: >>> >>> ERROR: left area data is missing >>> >>> I thought that the left area data is in the input dconn 32K dconn >>>cifti. >>> >>> Could you please have a look in the above command and advice on what i >>> am doing wrong? >>> >>> Thank you very much >>> >>> Best >>> >>> Giorgos >>> >>> >>> >>> >>> --- >>> This email has been checked for viruses by Avast antivirus software. >>> https://www.avast.com/antivirus >>> >>> _______________________________________________ >>> 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. If you have >>received this email in error, please immediately notify the sender via >>telephone or return mail. > > >--- >This email has been checked for viruses by Avast antivirus software. >https://www.avast.com/antivirus > ________________________________ 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. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
