COMMANDS.md

• atlasgray (overlay: integer; const filt: array of integer) Gray atlas areas. For example atlasgray(0,[3,7]) will gray-out areas 3 and 7 of the background atlas. On the other hand, atlashide(1,[2,5]) will gray-out areas 2 and 5 of the first overlay image. For example atlashide(0,[3,7]) will gray the areas 3 and 7 of the background atlas. On the other hand, atlashide(1,[2,5]) will gray areas 2 and 5 of the first overlay image. [Not compatible with Python]
• atlashide (overlay: integer; const filt: array of integer) Hide atlas areas. For example atlashide(0,[3,7]) will hide the areas 3 and 7 of the background atlas. On the other hand, atlashide(1,[2,5]) will hide areas 2 and 5 of the first overlay image. [Not compatible with Python]
• atlasmaxindex (overlay: integer): integer Reports maximum region humber in specified atlas. For example, if you load the CIT168 atlas (which has 15 regions) as your background image, then atlasmaxindex(0) will return 15.
• atlassaturationalpha (saturation, transparency: float) Set saturation and transparency of atlas. A desaturated atlas will appear gray, a transparent atlas will reveal the background color.
• atlasstatmap (atlasname, statname: string; const indices: array of integer; const intensities: array of single) This creates a new mesh, where indexed regions are saved having the corresponding brightness from the array 'indices'. For example atlasstatmap('jhu.mz3','',[1,3,9],[1.1, 4.4, 2.4]) creates a mesh where regions 1, 3, and 9 are given values 1.1, 4.4 and 2.4. If statname is provided, a mesh will be saved to disk, e.g. atlasstatmap('jhu.mz3','out.mz3',[1,3,9],[1.1, 4.4, 2.4]). nb this function is for creating maps, you can load them with loadmesh() and loadoverlay(). [Not compatible with Python]
• azimuth (degrees: integer) This command rotates the rendering.
• azimuthelevation (azi, elev: integer) Sets the viewer location.
• backcolor(r, g, b: integer) Changes the background color, for example backcolor(255, 0, 0) will set a bright red background
• bmpzoom (z: integer) copy and save bitmaps at higher resolution than screen. bmpzoom(2) will save images at twice the resolution.
• cameradistance (z: float) Sets the viewing distance from the object.
• camerapan (x, y: float) Translate image horizontally (x) and vertically (y). range -1..+1, where 0 is centered.
• clip (depth: float) Creates a clip plane that hides information close to the viewer.
• clipazimuthelevation (depth, azi, elev: float) Set a view-point independent clip plane.
• colorbarposition (pos: integer) Sets the position of the colorbar: 1=bottom, 2=left, 3=top, 4=right.
• colorbarvisible (visible: boolean) Shows a colorbar on the main images.
• edgecolor (name: string; varies: boolean) Select color scheme for connectome edge map
• edgecreate (filename: string; const mtx: array of single) Create a connectome edge map. For example, if you have 3 nodes, mtx should be an array with 9 values (3*3). For example, edgecreate('',[1,2,3, 2,4,5, 3,5,6]) creates the links between 3 regions. Note the lower triangle and diagonal of this matrix is ignored. [Not compatible with Python]
• edgeload (filename: string) Loads a BrainNet Viewer format Edge file, e.g. connectome map
• edgesize (size: float; varies: boolean) Set the diameters of the cylinders of the connectome.
• edgethresh (lo, hi: float) Set minimum and maximum values for connectome edge diameters.
• elevation (degrees: integer) Changes the render camera up or down.
• exists (filename: string): boolean Returns true if file exists on disk.
• fontname (filename) Changes font used for colorbar. For example, "fontname(''ubuntu'')" will use the Ubuntu font.
• meshcolor (r, g, b: integer) Set red/green/blue components of main image.
• meshcreate (niiname, meshname: string; threshold, decimateFrac: float; minimumClusterVox, smoothStyle: integer) Convert a NIfTI voxel-based image into a mesh
• meshcurv () Displays mesh curvature, so crevices appear dark.
• meshload (filename: string) Opens a mesh to view.
• meshoverlayorder (flip: boolean) If true, the mesh will be drawn after the overlay, and xray sliders will influence overlay not mesh.
• meshreversefaces() reverse triangle winding to reverse front/back faces
• meshsave (filename: string) Saves currently open mesh to disk.
• modalmessage (str: string) Shows a modal dialog, script stops until user presses 'OK' button to dismiss dialog.
• modelessmessage (str: string) Shows text in the bottom status region of the scripting window.
• nodecolor (name: string; varies: boolean) set colorscheme used for nodes.
• nodecreate (filename: string; const x, y, z, color, radius: array of single) Generates and displays a connectome hub map. The arrays x,y,z refer to the 3D spatial coordinates. The optional color and radius arrays allow you to specify the size. For example nodecreate('mynode.node',[0, 10, 8], [9, 0, 8], [0, 9, 0], [], []) creates three spheres with the default size and color. On the other hand, nodecreate('mynode.node',[0, 10, 8], [9, 0, 8], [0, 9, 0], [1, 2, 9], [5]) creates three spheres each with a unique color intensity and with a size of 5. [Not compatible with Python]
• nodehemisphere (val: integer) Set -1 for left hemipshere, 0 for both, 1 for right
• nodeload (filename: string) Loads BrainNet viewer format node file.
• nodepolarity (val: integer) Set -1 for negative only, 0 for either, 1 for positive only.
• nodesize (size: float; varies: boolean) Determine size scaling factor for nodes.
• nodethresh (lo, hi: float) Set the minimum and maximum range for nodes.
• nodethreshbysizenotcolor (NodeThresholdBySize: boolean) If true then nodes will be hidden if they are smaller than the provided threshold. If false, they will be hidden if their color intensity is below the provided threshold.
• orientcubevisible (visible: boolean) Show or hide cube that indicates object rotation
• overlayadditive (add: boolean) Determines whether overlay colors are combined by adding or mixing the colors. For example, overlap of red and green overlays will appear yellow if additive is true
• overlaycloseall () This function has no parameters. All open overlays will be closed.
• overlaycolorname (overlay: integer; filename: string) Set the colorscheme for the target overlay to a specified name.
• overlayinvert (overlay: integer; invert: boolean) toggle whether overlay color scheme is inverted.
• overlayload (filename: string) integer; Will add the overlay named filename and return the number of the overlay.
• overlayminmax (overlay: integer; min, max: float) Sets the color range for the overlay.
• overlaysmoothvoxelwisedata (smooth: boolean) Determines if overlays are loaded using interpolation (smooth) or nearest neighbor (un-smoothed) interpolation.
• overlaytranslucent (overlay: integer; translucent: boolean) The feature allows you to make individual overlays translucent or opaque.
• overlaytransparencyonbackground (percent: integer) Controls the opacity of the overlays on the background.
• overlayvisible (overlay: integer; visible: boolean) This feature allows you to make individual overlays visible or invisible.
• quit () Terminate application. Useful if another program is controlling this software
• resetdefaults () Sets all of the user adjustable settings to their default values.
• savebmp (filename: string) Saves the currently viewed image as a PNG format compressed bitmap image.
• scriptformvisible (visible: boolean) Shows/hides the scripting form.
• shaderadjust (property: string; value: float) Sets one of the user-adjustable properties.
• shaderambientocclusion (amount: float) Specify a value in the range 0..1 to set the strength of the crevice shadows
• shaderforbackgroundonly (onlybg: boolean) If true selected shader only influeces background image, otherwise shader influences background, overlays, tracks and nodes.
• shaderlightazimuthelevation (azimuth, elevation: integer) Changes location of light source.
• shadername (Filename: string) Loads the requested shader.
• shaderxray (object, overlay: float) See occluded overlays/tracks/nodes by making either object transparent (0..1) or overlay/tracks/nodes emphasized (0..1)
• trackload (filename: string) Load fiber steam lines from a file.
• trackprefs (length, width, dither: float) set the size and properties for streamlines
• version (): string Returns software version name.
• viewaxial (std: boolean) Creates rendering from an axial viewpoint.
• viewcoronal (std: boolean) Creates rendering from a coronal viewpoint.
• viewsagittal (std: boolean) creates rendering from an sagittal viewpoint.
• wait (msec: integer) The program pauses for the specified duration. For example WAIT(1000) delays the script for one second.