CONN mesh_display help


  conn_mesh_display surface display in CONN   conn_mesh_display(fileSURF) displays surface- or volume-level data in fileSURF projected to reference cortical surface       fileSURF         : surface- or volume- level 3D NIFTI file (values in this file will be projected and displayed on   the reference cortical surface -surfaces derived from the ICBM MNI 2009b NLIN asymmetric template-)   conn_mesh_display(fileSURF [,fileVOL, dirFS, rois, connections])        fileVOL          : volume-level 3D NIFTI mask file (display clusters of non-zero values as custom masks)       dirFS            : directory containing reference freesurfer-generated surfaces (leave empty for default conn/utils/surf/)       rois             : structure defining ROIs to be displayed                            rois.sph_xyz : (nx3) coordinates XYZ values                            rois.sph_c   : (nx3) color RGB values                            rois.sph_r   : (nx1) sphere radius       connections      : (nxn) matrix of ROI-to-ROI connections to be displayed (values represent connection                          strength, with 0 or NaN for connections not to be displayed)    fh = conn_mesh_display(...) returns function handle for additional options   VIEW OPTIONS   fh('view',viewdir [,viewpos,side])    : controls camera view                                            viewdir : camera direction (e.g. [1 0 0])                                            viewpos : camera-up vector []                                            side    : 0 both hemispheres; -1 left-hemisphere only; +1 right-hemisphere only   fh('copy')                            : copies current camera view   fh('paste')                           : paste camera view   fh('zoomin')                          : zoom-in display   fh('zoomout')                         : zoom-out display   fh('info')                            : shows details of fileSURF/fileVOL data being displayed    REFERENCE SURFACE OPTIONS    fh('brain',type);                    : chooses reference brain surface                                            type=1: White Matter                                            type=2: Grey Matter                                             type=3: Semi-inflated WM                                            type=4: Inflated WM   fh('brain_transparency',val)          : set reference brain surface transparency level (val: 0-1)   fh('brain_color')                     : set reference brain surface color   fh('repaint',filename)                : change reference brain surface activation file (filename: NIFTI file) (fileSURF)    fh('mask',state)                      : displays reference brain surface medial mask (state: 'on' 'off')   fh('act_transparency',val)            : set reference brain surface activation transparency level (val: 0-1)   fh('act_pos')                         : reference brain surface activation displays only positive acitivation values   fh('act_neg')                         : reference brain surface activation displays only negative acitivation values   fh('act_posneg')                      : reference brain surface activation displays both positive/negative acitivation values   fh('act_color',color)                 : reference brain surface activation color (color: [1x3] RGB values)   fh('sub',state)                       : displays reference subcortical surface (state: 'on' 'off')   fh('sub_transparency',val)            : set subcortical surface transparency level (val: 0-1)   fh('sub_color',color)                 : set subcortical surface color (color: [1x3] RGB values)   fh('brainmask_transparency',val)      : set brainmask surface transparency level (val: 0-1)   fh('brainmask_color',color)           : brainmask surface activation color (color: [1x3] RGB values)   fh('ref_sag',state)                   : displays reference sagittal slice (state: 'on' 'off')   fh('ref_cor',state)                   : displays reference coronal slice (state: 'on' 'off')   fh('ref_ax',state)                    : displays reference axial slice (state: 'on' 'off')   fh('ref_transparency',val)            : set reference slices transparency level (val: 0-1)   fh('ref_pos',pos)                     : set reference slices position (pos: [1x3] vector of x/y/z coordinates)   fh('ud_select',filename)              : adds custom reference surface (filename: NIFTI mask file)   fh('ud_delete')                       : removes last custom reference surface   fh('ud_transparency',val)             : set custom reference surface transparency level (val: 0-1)   fh('ud_color',color)                  : set custom reference surface color (color: [1x3] RGB values)   ROI OPTIONS   fh('roi_transparency',val)            : set ROIs surface transparency level (val: 0-1)   fh('roi_color',color)                 : set ROIs surface color (color: [Mx3] RGB values)   fh('sphereshape',type)                : set ROI shape (type: 'sphere' 'cube' 'star')   fh('spheres',scale)                   : increases/decreases all ROIs size (scale 0-inf)   fh('labels',state)                    : displays ROI labels (state: 'on' 'off')   fh('labels_font',scale)               : increases/decreases all ROI-labels font (scale 0-inf)   fh('labels_edit',labels)              : changes ROI labels (labels: cellstring array)   fh('con_transparency',val)            : set connectivity-lines transparency level (val: 0-1)   fh('con_color',color)                 : set connectivity-lines color (color: [1x3] RGB values)   fh('con_bundling',level)              : set connectivity-lines bundling level (level: integers 0-inf)   fh('con_width',scale)                 : increases/decreases all connectivity-lines width (scale 0-inf)   EFFECTS OPTIONS   fh('material',option)                 : sets material reflectance mode (option: 'dull' 'shiny' 'metal' [1x5]; see "help material")   fh('light',level)                     : sets lighting strength (level: 0-1)   fh('background',color)                : sets background color (color: [1x3] RGB values)   fh('colorbar',state)                  : displays reference colorbar (state: 'on' 'off')   fh('colorbar','rescale',lim)          : changes activation colorbar limits (lim: [1x2] values in fileSURF NIFTI file)   fh('colormap',type)                   : changes activation colormap (type: 'normal','red','jet','hot','gray','bone','cool','hsv','spring','summer','autumn','winter','random','brighter','darker','manual','color')   fh('smoother',state)                  : 'on' for smoother display (interpolates values in fileSURF NIFTI file when displaying on surface); 'off' for raw-data display   fh('axis',state)                      : display reference axis lines (state: 'on' 'off')   fh('menubar',state)                   : display menubar (state: 'on' 'off')   PRINT OPTIONS   fh('print',type,filename)             : prints display to high-resolution .jpg file                                            type=1: prints current view                                            type=2: prints 2-view row display (left&right exterior views)                                            type=3: prints 3-view mosaic display (superior,right,posterior views; e.g. glass-displays)                                            type=4: prints 4-view mosaic display (left, right, medial-left, medial-right views)                                            type=5: prints 4-view column display (same as above all views in a single column)                                            type=6: prints 4-view row display (same as above all views in a single row)                                            type=7: prints 8-view mosaic display (left, right, medial-left, medial-right, superior, inferior, anterior, posterior views)