Thanks a lot for the suggestion Timothy. Unfortunately I'm still getting a colourless map. I did get the result I wanted using the matlab gifti toolbox ( http://www.artefact.tk/software/matlab/gifti/ ), so no rush.
Perhaps I'm saving under the wrong name, or doing something wrong when trying to visualise? Here's the actual command I'm using. wb_command -volume-label-import sequential_region_map_no_hipp.nii.gz hipp_pre_color_palette_table.txt sequential_region_map_no_hipp_ hcp_label.nii.gz Then when I'm trying to visualise it, I'm just loading it in and trying to display over the atlas I'm using. Not sure if there's more info I can give. Thanks again for the help. Best wishes, Sean On 21 June 2017 at 11:42, Timothy Coalson <tsc...@mst.edu> wrote: > The fourth "color" specifier in your text file should be 255, not 1. > > Tim > > > On Wed, Jun 21, 2017 at 8:34 AM, Seán Froudist Walsh <froud...@tcd.ie> > wrote: > >> Sorry, made a mistake in my e-mail. I tried wb_command >> -volume-label-import and got the results explained previously. Any ideas? >> >> Thanks, >> >> Sean >> >> On 20 June 2017 at 20:08, Glasser, Matthew <glass...@wustl.edu> wrote: >> >>> I think you want wb_command -volume-label-import. >>> >>> Peace, >>> >>> Matt. >>> >>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Seán >>> Froudist Walsh <froud...@tcd.ie> >>> Date: Tuesday, June 20, 2017 at 7:04 PM >>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>> Subject: [HCP-Users] Custom visualisation help >>> >>> Hey all, >>> >>> I'm trying to get a colour display on a surface to match a colormap I >>> have set up in matlab, and have run into a whole world of pain. I would >>> greatly appreciate your help. >>> >>> I have created a label text file of the following format: >>> >>> TCpol_R >>> 1 255 208 208 1 >>> TCs_R >>> 2 255 158 158 1 >>> Amyg_R >>> 3 255 81 81 1 >>> PFCoi_R >>> 4 255 231 231 1 >>> >>> I additionally have a nifti file, and a func.gii surface file (created >>> with wb_command -volume-to-surface-mapping ) >>> >>> Ideally I would like to display those colours on the surface, in the >>> correct clusters. >>> >>> I thought I would try to display them on a volume as a first step, but >>> that hasn't gone smoothly either. >>> I used a command of the following format: >>> wb_command -cifti-label-import my_atlas.nii.gz my_label_table.txt >>> my_label_volume.nii.gz >>> >>> Then I tried to display the label file over the volume in wb_view to no >>> avail (I only see the underlying anatomical volume). Despite this, if I go >>> to >>> Overlay Tools --> Settings --> Edit Map's Labels >>> I can see all of the labels I wanted listed, next to the correct >>> colours. >>> >>> I would greatly appreciate if you could help fill in the gaps in my >>> knowledge so that I can display my custom coloured labels on the surface. >>> >>> Many thanks, >>> >>> Sean >>> >>> _______________________________________________ >>> 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 >> > > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
