Thanks
On 7/16/2016 5:03 PM, Glasser, Matthew wrote: > 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. 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