Dear Fred,

You could use the syntax (this is for version 15b, I took the opportunity to simplify a bit the calling syntax of this function in the latest release):

  conn_mesh_display('', '', '', XYZ, R, .2);

where XYZ is a [N by 3] matrix containing the x/y/z coordinates (in MNI mm) of N ROIs, and R is a [N by N] matrix containing the correlation strengths between your ROIs (set to 0 those connections that you wish not to be displayed)

If, in addition, you want to control the size and color of each ROI sphere, define XYZ to be a structure with fields:
  sph_xyz:  [N by 3] matrix of ROI coordinates (xyz mm values)
  sph_r:      [N by 1] vector of sphere radius
  sph_c:      [N by 3] matrix of sphere colors (rgb 0-1 values)

The other input parameters in conn_mesh_display are:

  conn_mesh_display( filenameSURF, filenameVOL, freesurferFolder, XYZ, R, alpha)
     filenameSURF: .img/.nii file containing 'activation' values to be displayed at the brain surface (from volume- or surface- based analyses) (e.g. as in the 'Display Surface' option in the second-level results explorer)
     filenameVOL: .img/.nii file containing mask to be displayed as 'activation blobs' (e.g. as in the 'Display Volume' option in the second-level results explorer)
     freesurferFolder: location of surface files used for brain displays (defaults to conn/utils/surf)
     alpha: initial transparency value for brain display (this, as well as many other display options, can be later modified in the GUI)

Hope this helps
Alfonso
 
Originally posted by fred Sampedro: