The command should (and for me, does) work without telling it to smooth. Make sure you are using the latest version (v1.0 currently). I don't suppose the input file is a constant everywhere? Please run -file-information on the input and output files (surface and metric).
I would expect caret5 to throw an error when not given a topology file, but maybe it is grabbing the hidden topology file in the coordinate header (don't ask). Topology is needed for gradient, it needs to know what the neighbors are. The .surf.gii files we use now contain both coordinates and topology, which is why workbench doesn't need topology files. Tim On Fri, Oct 17, 2014 at 7:11 AM, Glasser, Matthew <[email protected]> wrote: > You should not be using the inflated surface (rather the midthickness > surface would be more appropriate). It is possible that the command does > not work correctly without a little pre-smoothing but Tim will need to > comment on that. > > Peace, > > Matt. > > On 10/17/14, 5:29 AM, "K. Wagstyl" <[email protected]> wrote: > > >Hi HCP-users list, > > > >I'm having trouble using the metric gradient command. > > > >Using workbench: > >wb_command -metric-gradient 1.L.inflated.164k_fs_LR.surf.gii > >1.L.thickness.164k_fs_LR.shape.gii > >1.L.thicknessgradient.164k_fs_LR.shape.gii > > > >Or Caret: > >caret_command -metric-gradient 1.L.inflated.164k_fs_LR.coord.gii NULL > >1.L.thickness.164k_fs_LR.shape.gii 1 1.L.gradient.164k_fs_LR.shape.gii > >NULL 1 true 3 > > > >Either the commands don't run or the magnitude is returned as zeros. > >Could I check what the input files ought to be? > > > > > >Thanks, > >Konrad > >_______________________________________________ > >HCP-Users mailing list > >[email protected] > >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. > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
