CONN mesh_display help

conn_mesh_display

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)

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