search

MRtrix3 / mrtrix3

MRtrix3 provides a set of tools to perform various advanced diffusion MRI analyses, including constrained spherical deconvolution (CSD), probabilistic tractography, track-density imaging, and apparent fibre density
http://www.mrtrix.org
Mozilla Public License 2.0
294 stars 181 forks source link

convert Connectome to Glass brain visualisation #2415

Open Meryam1985 opened 2 years ago

Meryam1985 commented 2 years ago

Hello I am trying to convert Connectome to a glass brain like this figure: image I have some trouble using the plotting.plot_connectome (corr_arr, coords, title = 'test correlation graph', edge_threshold = "99.7%", node_size = 20, node_color = color_networks, colorbar = True). I want help, regarding the glass brain tracing corresponding to the correlation matrix from diffusion imaging (MRTRIX3). So, how to use /usr/local/mrtrix3/share/mrtrix3/labelconvert/fs_default.txt to define the coordinates ,or are there others solutions? Cordially.

Lestropie commented 2 years ago

If what you're looking for is simply appropriate coordinates at which each node should be drawn, this is impossible to determine from file fs_default.txt, since it does not contain any position information. What I think might serve your needs (though it may require some reformatting to be compatible with whatever software you are using) is using the labelstats command on an exemplar parcellation image.