Use -volume-label-import on the file. If you specify "" as the text file name, it will assign random colors to each integer.
Tim On Thu, Mar 30, 2017 at 7:59 PM, Dev vasu < vasudevamurthy.devulapa...@gmail.com> wrote: > Dear Sir, > > Each label consists of several hippocampus subfield already marked with > different integers as stated here https://github.com/CobraLab/ > atlases/tree/master/hippocampus-subfields. > > > I am interested in visualizing each of the sub field in the label with > marked integers values. > > Thanks > Vasudev > > On 31 March 2017 at 00:31, Timothy Coalson <tsc...@mst.edu> wrote: > >> 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 <vasudevamurthy.devulapally@gm >> ail.com> 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/an >>> tsRegistration-MAGeT . >>> >>> >>> Thanks >>> Vasudev >>> >>> On 30 March 2017 at 22:46, Timothy Coalson <tsc...@mst.edu> 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.devulapa...@gmail.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 >>>>> 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
