It looks like that method outputs each label as a separate file, which is important information for understanding what your question is. I suggest combining them into one file with different integers for each label.
One way to do this is to use -volume-merge to turn the labels into a multi-frame volume file, then use -volume-reduce INDEXMAX and MAX to generate the file of integers, and a file you can mask out unlabeled areas with (using -volume-math). Then use -volume-label-import to give them names and colors. Tim On Thu, Mar 30, 2017 at 5:03 PM, Dev vasu < [email protected]> wrote: > Dear Sir, > > > I am not experiencing any problem but i am unable to see different colour > maps in label files ( in .nii format ) , The labels are Hippocampus > subfields which i have segmented using https://github.com/CobraLab/ > antsRegistration-MAGeT . > > > Thanks > Vasudev > > On 30 March 2017 at 22:46, Timothy Coalson <[email protected]> wrote: > >> That isn't what -label-to-volume-mapping does, it requires a *surface* >> label file (gifti) as input. >> >> wb_view should be able to load most nifti volume files, and it isn't >> clear what kind of problem you are having (is there an error message? does >> it show up in the save/manage files dialog?). What created the file? >> >> If you just have a volume file with integers in it, you can load it >> as-is, but similar integers will get similar colors, which may not be >> desired. You can use -volume-label-import on such a volume file to create >> a workbench-format nifti label volume that allows you to set each label's >> color and name independently. >> >> Tim >> >> >> On Thu, Mar 30, 2017 at 1:53 PM, Dev vasu <vasudevamurthy.devulapally@gm >> ail.com> wrote: >> >>> Dear all, >>> >>> I have label files in nifti format and i am unable to visualize color >>> bars and associated labels , should i refine the labels using >>> *-label-to-volume-mapping >>> *and is there any mandatory naming convention and format ( NIFITI or >>> GIFTI ) for Connectome workbench to recognize the labels ?. >>> >>> >>> >>> Thanks >>> Vasudev >>> >>> >>> _______________________________________________ >>> 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
