Re: [HCP-Users] Separating Parcellated Files
Oh good to know! Thanks Tim! Best, -Tim On Mon, Feb 18, 2019 at 5:39 PM Timothy Coalson wrote: > Parcellated files contain only one value per parcel (per map), so it isn't > a good idea to try to reconstitute them into a spatial map before > analysis. I think the correct thing to do is to put them through PALM in a > way that doesn't use spatial information (no tfce, no smoothing, etc). > > Tim > > > On Mon, Feb 18, 2019, 4:27 PM Timothy Hendrickson > wrote: > >> Hello, >> >> I am attempting to perform an analysis with the tool PALM with >> parcellated surface data. Within the PALM wiki underneath the CIFTI >> examples portion it is suggested to separate cifti files into it's discrete >> pieces, so I tried to separate the parcellated file into the left and right >> hemisphere, however I get a failure. >> >> /home/lnpi14-raid1/timothy-data-lnpi14/DOWNLOADS/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command >> -cifti-separate merged_MyelinMap_MSMSulc.Glasser.pscalar.nii ROW -metric >> CORTEX_LEFT merged_MyelinMap_MSMSulc.Glasser.L.func.gii -metric >> CORTEX_RIGHT merged_MyelinMap_MSMSulc.Glasser.R.func.gii >> >> ERROR: specified direction does not contain brain models >> >> While running: >> /home/lnpi14-raid1/timothy-data-lnpi14/DOWNLOADS/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command >> -cifti-separate merged_MyelinMap_MSMSulc.Glasser.pscalar.nii COLUMN -metric >> CORTEX_LEFT merged_MyelinMap_MSMSulc.Glasser.L.func.gii -metric >> CORTEX_RIGHT merged_MyelinMap_MSMSulc.Glasser.R.func.gii >> >> ERROR: specified direction does not contain brain models >> >> Any suggestions? >> >> Thank you! >> >> -Tim >> >> >> Timothy Hendrickson >> Neuroimaging Analyst/Staff Scientist >> University of Minnesota Informatics Institute >> University of Minnesota >> Bioinformatics M.S. Candidate >> Office: 612-624-0783 >> Mobile: 507-259-3434 (texts okay) >> >> ___ >> 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
Re: [HCP-Users] Separating Parcellated Files
Parcellated files contain only one value per parcel (per map), so it isn't a good idea to try to reconstitute them into a spatial map before analysis. I think the correct thing to do is to put them through PALM in a way that doesn't use spatial information (no tfce, no smoothing, etc). Tim On Mon, Feb 18, 2019, 4:27 PM Timothy Hendrickson wrote: > Hello, > > I am attempting to perform an analysis with the tool PALM with parcellated > surface data. Within the PALM wiki underneath the CIFTI examples portion it > is suggested to separate cifti files into it's discrete pieces, so I tried > to separate the parcellated file into the left and right hemisphere, > however I get a failure. > > /home/lnpi14-raid1/timothy-data-lnpi14/DOWNLOADS/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command > -cifti-separate merged_MyelinMap_MSMSulc.Glasser.pscalar.nii ROW -metric > CORTEX_LEFT merged_MyelinMap_MSMSulc.Glasser.L.func.gii -metric > CORTEX_RIGHT merged_MyelinMap_MSMSulc.Glasser.R.func.gii > > ERROR: specified direction does not contain brain models > > While running: > /home/lnpi14-raid1/timothy-data-lnpi14/DOWNLOADS/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command > -cifti-separate merged_MyelinMap_MSMSulc.Glasser.pscalar.nii COLUMN -metric > CORTEX_LEFT merged_MyelinMap_MSMSulc.Glasser.L.func.gii -metric > CORTEX_RIGHT merged_MyelinMap_MSMSulc.Glasser.R.func.gii > > ERROR: specified direction does not contain brain models > > Any suggestions? > > Thank you! > > -Tim > > > Timothy Hendrickson > Neuroimaging Analyst/Staff Scientist > University of Minnesota Informatics Institute > University of Minnesota > Bioinformatics M.S. Candidate > Office: 612-624-0783 > Mobile: 507-259-3434 (texts okay) > > ___ > 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
[HCP-Users] Separating Parcellated Files
Hello, I am attempting to perform an analysis with the tool PALM with parcellated surface data. Within the PALM wiki underneath the CIFTI examples portion it is suggested to separate cifti files into it's discrete pieces, so I tried to separate the parcellated file into the left and right hemisphere, however I get a failure. /home/lnpi14-raid1/timothy-data-lnpi14/DOWNLOADS/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command -cifti-separate merged_MyelinMap_MSMSulc.Glasser.pscalar.nii ROW -metric CORTEX_LEFT merged_MyelinMap_MSMSulc.Glasser.L.func.gii -metric CORTEX_RIGHT merged_MyelinMap_MSMSulc.Glasser.R.func.gii ERROR: specified direction does not contain brain models While running: /home/lnpi14-raid1/timothy-data-lnpi14/DOWNLOADS/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command -cifti-separate merged_MyelinMap_MSMSulc.Glasser.pscalar.nii COLUMN -metric CORTEX_LEFT merged_MyelinMap_MSMSulc.Glasser.L.func.gii -metric CORTEX_RIGHT merged_MyelinMap_MSMSulc.Glasser.R.func.gii ERROR: specified direction does not contain brain models Any suggestions? Thank you! -Tim Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users