Then do as Tim suggests. Matt.
From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Dev vasu <vasudevamurthy.devulapa...@gmail.com<mailto:vasudevamurthy.devulapa...@gmail.com>> Date: Thursday, March 30, 2017 at 7:59 PM To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Cc: "<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] wb_view : Unable to load labels through features tab 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<mailto: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.devulapa...@gmail.com<mailto:vasudevamurthy.devulapa...@gmail.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/antsRegistration-MAGeT . Thanks Vasudev On 30 March 2017 at 22:46, Timothy Coalson <tsc...@mst.edu<mailto: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<mailto: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<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
