Hi Tim and Matt, It seems to be working fine now. The key changes were converting from caret to workbench formats and using the mid thickness surface. Is the effect of curvature (gyri and sulci) automatically regressed out is this done manually afterwards? Cheers, Konrad On 20 Oct 2014, at 11:04, Konrad Wagstyl <[email protected]> wrote:
> Hi Tim and Matt, > > Thanks for the help. The wb gradient command now works fine on hcp data but > not on external data. > We've been using the caret fs_to_LR pipeline to convert the data from > freesurfer. Is there now an equivalent freesurfer to workbench pipeline? > I've tried editing the HCP general pipeline but am getting stuck with naming > convention issues. Is there a script somewhere else that I might have missed? > > Thanks, > Konrad > > On 17 Oct 2014, at 21:07, Timothy Coalson <[email protected]> wrote: > >> 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
