{"action":"opened","issue":{"url":"https://api.github.com/repos/ThomasYeoLab/CBIG/issues/4","repository_url":"https://api.github.com/repos/ThomasYeoLab/CBIG","labels_url":"https://api.github.com/repos/ThomasYeoLab/CBIG/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/ThomasYeoLab/CBIG/issues/4/comments","events_url":"https://api.github.com/repos/ThomasYeoLab/CBIG/issues/4/events","html_url":"https://github.com/ThomasYeoLab/CBIG/issues/4","id":405656505,"node_id":"MDU6SXNzdWU0MDU2NTY1MDU=","number":4,"title":"Network ordering of Kong2018_MSHBM","user":{"login":"rubykong","id":20438248,"node_id":"MDQ6VXNlcjIwNDM4MjQ4","avatar_url":"https://avatars3.githubusercontent.com/u/20438248?v=4","gravatar_id":"","url":"https://api.github.com/users/rubykong","html_url":"https://github.com/rubykong","followers_url":"https://api.github.com/users/rubykong/followers","following_url":"https://api.github.com/users/rubykong/following{/other_user}","gists_url":"https://api.github.com/users/rubykong/gists{/gist_id}","starred_url":"https://api.github.com/users/rubykong/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rubykong/subscriptions","organizations_url":"https://api.github.com/users/rubykong/orgs","repos_url":"https://api.github.com/users/rubykong/repos","events_url":"https://api.github.com/users/rubykong/events{/privacy}","received_events_url":"https://api.github.com/users/rubykong/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2019-02-01T11:11:23Z","updated_at":"2019-02-01T11:11:23Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"We are trying to release a few scripts to provide the network label with the network name. \r\nThe only problem might be that the network structure could be very different if you are training from scratch on a different dataset. Here are two cases:\r\n\r\n#### Use our estimated group priors to estimate individual parcellation\r\nThe group atlas will be utilized to initialize the algorithm, therefore, the network order in the individual parcellation will be the same as the group parcellation.\r\nWe provided two group priors which are generated by a group atlas estimated by GSP dataset in fsaverage5 space, and a group atlas estimated by HCP dataset in fsLR_32k space. \r\nI will provide these group atlases with corresponding network labels. \r\n\r\n#### Use your own data to train the model and estimate group priors\r\nIf you train on your own data, then your group atlas will be different from ours, the network ordering will also be different. In this way, you will have to run a Hungarian match algorithm to match the networks in your estimated group atlas with our atlases. \r\nTo do that, you can use the following code:\r\n\r\n1) If it's fsaverage5, you can directly use the following command to reorder the color table and visualize it:\r\n```\r\nmy_par = load('<output_dir>/group/group.mat');\r\nref_par = load('/Kong2019_MSHBM/examples/results/estimate_group_priors/group/group.mat');\r\n[output, assign, cost, dice_overlap] = CBIG_HungarianClusterMatch([ref_par.lh_labels; ref_par.rh_labels], [my_par.lh_labels; my_par.rh_labels], 1);\r\ncolors_old=ref_par.colors(2:end,:);\r\ncolors_new=colors_old(assign,:);\r\ncolors_new=[[0,0,0];color_new];\r\nCBIG_DrawSurfaceMaps(my_par.lh_labels, my_par.rh_labels, 'fsaverage5', 'inflated',-Inf,Inf,colors_new);\r\n```\r\n\r\n2) If your data is in fslr, sorry, I didn't release the HCP group atlas in the current release (will do it asap), so contact me (roo.cone@gmail.com) to get the group atlas file `HCP_40sub_1000iter_17nets_cen_sm4.mat`.\r\n```\r\nmy_par = load(fullfile(output_dir,'group','group.mat'));\r\nref_par = load('HCP_40sub_1000iter_17nets_cen_sm4.mat');\r\n[output, assign, cost, dice_overlap] = CBIG_HungarianClusterMatch([ref_par.lh_labels; ref_par.rh_labels], [my_par.lh_labels; my_par.rh_labels], 1);\r\ncolors_old=ref_par.colors(2:end,:);\r\ncolors_new=colors_old(assign,:);\r\nCBIG_DrawSurfaceMaps_fslr(my_par.lh_labels, my_par.rh_labels, 'fs_LR_32k', 'inflated',-Inf,Inf,colors_new);\r\n```\r\nI will try to release all above commands and other useful scripts later this month.\r\n\r\n"}}
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