Skip to content

Latest commit

 

History

History
executable file
·
78 lines (74 loc) · 9.32 KB

COMMANDS.md

File metadata and controls

executable file
·
78 lines (74 loc) · 9.32 KB

Functions

Running the help menu item listed in the Scripting Menu's Templates menu will generate a comprehensive list of the available functions:

  • atlashide (built-in function): atlashide(layer, indices...) -> Hide all (e.g. "atlashide(1)") or some (e.g. "atlashide(1, (17, 22))") regions of an atlas.
  • atlaslabels (built-in function): atlasmaxindex(layer) -> Returns string listing all regions in an atlas
  • atlasmaxindex (built-in function): atlasmaxindex(layer) -> Returns maximum region number 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.
  • atlasshow (built-in function): atlasshow(layer, indices...) -> Show all (e.g. "atlasshow(1)") or some (e.g. "atlasshow(1, (17, 22))") regions of an atlas.
  • azimuthelevation (built-in function): azimuthelevation(azi, elev) -> Sets the render camera location.
  • backcolor (built-in function): backcolor(r, g, b) -> changes the background color, for example backcolor(255, 0, 0) will set a bright red background
  • bmptransparent (built-in function): bmptransparent(v) -> set if bitmaps use transparent (1) or opaque (0) background
  • bmpzoom (built-in function): bmpzoom(z) -> changes resolution of savebmp(), for example bmpzoom(2) will save bitmaps at twice screen resolution
  • cameradistance (built-in function): cameradistance(z) -> Sets the viewing distance from the object.
  • clipazimuthelevation (built-in function): clipazimuthelevation(depth, azi, elev) -> Set a view-point independent clip plane.
  • clipthick (built-in function): clipthick(thick) -> Set size of clip plane slab (0..1).
  • colorbarposition (built-in function): colorbarposition(p) -> Set colorbar position (0=off, 1=top, 2=right).
  • colorbarsize (built-in function): colorbarsize(p) -> Change width of color bar f is a value 0.01..0.5 that specifies the fraction of the screen used by the colorbar.
  • coloreditor (built-in function): coloreditor(s) -> Show (1) or hide (0) color editor and histogram.
  • colorfromzero (built-in function): colorfromzero(layer, isFromZero) -> Color scheme display range from zero (1) or from threshold value (0)?
  • colorname (built-in function): colorname(colorName) -> Loads the requested colorscheme for the background image.
  • colornode (built-in function): colornode(layer, index, intensity, r, g, b, a) -> Adjust color scheme for image.
  • cutout (built-in function): cutout(L,A,S,R,P,I) -> Remove sector from volume.
  • drawload (built-in function): drawload(filename) -> Load an image as a drawing (region of interest).
  • extract (built-in function): extract(b,s,t) -> Remove haze from background image. Blur edges (b: 0=no, 1=yes, default), single object (s: 0=no, 1=yes, default), threshold (t: 1..5=high threshold, 5 is default, higher values yield larger objects)
  • fullscreen (built-in function): fullscreen(max) -> Form expands to size of screen (1) or size is maximized (0).
  • generateclusters (built-in function): generateclusters(layer, thresh, minClusterMM3, method, bimodal) -> create list of distinct regions. Optionally provide cluster intensity, minimum cluster size, neighbor method(1=faces,2=faces+edges,3=faces+edges+corners). If bimodal = 1, both dark and bright clusters are detected.
  • graphscaling (built-in function): graphscaling(type) -> Vertical axis of graph is raw (0), demeaned (1) normalized -1..1 (2) normalized 0..1 (3) or percent (4).
  • gui_input (built-in function):
  • gui_input(caption, prompt, default) -> allow user to type value into a dialog box.
  • hiddenbycutout (built-in function): hiddenbycutout(layer, isHidden) -> Will cutout hide (1) or show (0) this layer?
  • invertcolor (built-in function): invertcolor(layer, isInverted) -> Is color intensity inverted (1) or not (0) this layer?
  • linecolor (built-in function): linecolor(r,g,b) -> Set color of crosshairs, so "linecolor(255,0,0)" will use bright red lines.
  • linewidth (built-in function): linewidth(wid) -> Set thickness of crosshairs used on 2D slices.
  • loadgraph (built-in function): loadgraph(graphName, add = 0) -> Load text file graph (e.g. AFNI .1D, FSL .par, SPM rp_.txt). If "add" equals 1 new graph added to existing graph
  • loadimage (built-in function): loadimage(imageName) -> Close all open images and load new background image.
  • minmax (built-in function): minmax(layer, min, max) -> Sets the color range for the overlay (layer 0 = background).
  • modalmessage (built-in function): modalmessage(msg) -> Show a message in a dialog box, pause script until user presses "OK" button.
  • mosaic (built-in function): mosaic(mosString) -> Create a series of 2D slices.
  • opacity (built-in function): opacity(layer, opacityPct) -> Make the layer (0 for background, 1 for 1st overlay) transparent(0), translucent (~50) or opaque (100).
  • orthoviewmm (built-in function): orthoviewmm(x,y,z) -> Show 3 orthogonal slices of the brain, specified in millimeters.
  • overlayadditiveblending (built-in function): overlayadditiveblending(v) -> Merge overlays using additive (1) or multiplicative (0) blending.
  • overlaycloseall (built-in function): overlaycloseall() -> Close all open overlays.
  • overlaycount (built-in function): overlaycount() -> Return number of overlays currently open.
  • overlayload (built-in function): overlayload(filename) -> Load an image on top of prior images.
  • overlayloadsmooth (built-in function): overlayloadsmooth(0) -> Will future overlayload() calls use smooth (1) or jagged (0) interpolation?
  • overlaymaskwithbackground (built-in function):
  • overlaymaskwithbackground(v) -> hide (1) or show (0) overlay voxels that are transparent in background image.
  • pitch (built-in function): pitch(degrees) -> Sets the pitch of object to be rendered.
  • quit (built-in function): quit() -> Terminate the application.
  • removesmallclusters (built-in function): removesmallclusters(layer, thresh, mm, neighbors) -> only keep clusters where intensity exceeds thresh and size exceed mm. Clusters based on neighbors that share faces (1), faces+edges (2) or faces+edges+corners (3)
  • resetdefaults (built-in function): resetdefaults() -> Revert settings to sensible values.
  • savebmp (built-in function): savebmp(pngName) -> Save screen display as bitmap. For example "savebmp('test.png')"
  • saveimg (built-in function): saveimg(filename) -> Save background image (layer 0) to disk. For example "saveimg('test.nii')", extension defines type (.nii=NIfTI, .osp=ospray, .bvox=blender)
  • scriptformvisible (built-in function): scriptformvisible (visible) -> Show (1) or hide (0) the scripting window.
  • shaderadjust (built-in function): shaderadjust(sliderName, sliderValue) -> Set level of shader property. Example "gl.shaderadjust('edgethresh', 0.6)"
  • shaderlightazimuthelevation (built-in function): shaderlightazimuthelevation(a,e) -> Position the light that illuminates the rendering. For example, "shaderlightazimuthelevation(0,45)" places a light 45-degrees above the object
  • shadermatcap (built-in function): shadermatcap(name) -> Set material capture file (assumes "matcap" shader. For example, "shadermatcap('mc01')" selects mc01 matcap.
  • shadername (built-in function): shadername(name) -> Choose rendering shader function. For example, "shadername('mip')" renders a maximum intensity projection.
  • shaderquality1to10 (built-in function): shaderquality1to10(i) -> Renderings can be fast (1) or high quality (10), medium values (6) balance speed and quality.
  • shaderupdategradients (built-in function): shaderupdategradients() -> Recalculate volume properties.
  • sharpen (built-in function): sharpen() -> apply unsharp mask to background volume to enhance edges
  • smooth (built-in function): smooth2D(s) -> make 2D images blurry (linear interpolation, 1) or jagged (nearest neighbor, 0).
  • sobel (built-in function): sobel(layer) -> Creates new layer based on Sobel edge map of selected layer.
  • toolformvisible (built-in function): toolformvisible(visible) -> Show (1) or hide (0) the tool panel.
  • version (built-in function): version() -> Return the version of MRIcroGL.
  • view (built-in function): view(v) -> Display Axial (1), Coronal (2), Sagittal (4), Flipped Sagittal (8), MPR (16), Mosaic (32) or Rendering (64)
  • viewaxial (built-in function): viewaxial(SI) -> Show rendering with camera superior (1) or inferior (0) of volume.
  • viewcoronal (built-in function): viewcoronal(AP) -> Show rendering with camera posterior (1) or anterior (0) of volume.
  • viewsagittal (built-in function): viewsagittal(LR) -> Show rendering with camera left (1) or right (0) of volume.
  • volume (built-in function): volume(layer, vol) -> For 4D images, set displayed volume (layer 0 = background; volume 0 = first volume in layer).
  • wait (built-in function): wait(ms) -> Pause script for (at least) the desired milliseconds.
  • windowposition (built-in function): windowposition(l,t,w,h) -> Set the left, top, width and height for the executable window.
  • yoke (built-in function): yoke(v) -> Yoke (1) instances so different instances show same view.
  • zerointensityinvisible (built-in function): zerointensityinvisible(layer, bool) -> For specified layer (0 = background) should voxels with intensity 0 be opaque (bool= 0) or transparent (bool = 1).
  • zoomcenter (built-in function): zoomcenter(x,y,z) -> Set center of expansion for zoom scale (values in range 0..1 with 0.5 in volume center).
  • zoomscale (built-in function): zoomscale2D(z) -> Enlarge 2D image (range 1..6).