On Mon, Oct 20, 2014 at 5:04 AM, 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. > Would you mind explaining what you changed that fixed it? Using the inflated surface should still give a result, just one that is not as biologically relevant. > 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? > Workbench will read most of caret5's metric files, though you might need to rename them to end in .func.gii for the GUI to recognize them. wb_import or caret_command -file-convert should be able to convert from caret5's formats (you want XML_BASE64_GZIP for metric, GS for surfaces, and nifti for volumes). Getting things out of freesurfer formats often involves mris_convert. > 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
