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NeuroElf - global configuration (variable)


For the purpose of keeping a globally accessible configuration, a single 1×1 struct variable, ne_gcfg, stores settings and this wiki page describes the more important ones as a reference for scripting functionality

Coarse structure

The structure ne_gcfg contains the following fields (all of which are 1×1 struct variables, unless otherwise noted):

  • .c - global run-time, UI, and @xini-based configuration, error handling, etc.
  • .cc - child-window configuration (undocked windows, beta plotter, etc.)
  • .fcfg - figure-based configuration and @xff handle shortcuts, including sub-structures for general UI dialogs
  • .h - @xfigure and Matlab UI handle shortcuts (equally including sub-structures for dialogs)
  • .lut - LUT (@xff) object with lookup-table colors for VMR overlay
  • .poi - POI (@xff) object with cluster-table for surface-based objects
  • .tio - structure with @transimg handles used in main UI (slices, render)
  • .voi - VOI (@xff) object with cluster-table for voxel-based objects
  • .w and .wc - workspace (loaded @xff objects in main UI)

Figure-based configuration

The subfield ne_gcfg.fcfg contains the fields described below (any fields in the structure not mentioned here either have no functionality or will be removed shortly).

Fixed child-dialogs (single instance allowed per dialog)

These dialogs' configurations are described in greater detail on their own pages.

Main UI configuration settings

  • .asimthr - thresholds passed into alphasim(VOLUME_SIZE, struct('thr', ASIMTHR, …))
  • .chair - status of cross-hair visibility (read-only)
  • .chcol - cross-hair color (read-only)
  • .clconn - cluster-connectivity setting (for OBJ::ClusterTable(MAP_NUMBER, MAP_THRESHOLD, struct('clconn', CLCONN, …)))
  • .clim - cluster-restriction limitation (for VOI::Combine(LIST_OF_VOIS, 'restrict', struct('rsize', CLIM, …)))
  • .clsort - cluster-sorting algorithm (for OBJ::ClusterTable(MAP_NUMBER, MAP_THRESHOLD, struct('sorting', CLSORT, …)))
  • .cpos - current position (in real-world mm, read-only)
  • .cstep - step applied to coordinate when using the cursor keys (set by changing the current object, read-write)
  • .ddir - last drawing direction (read-only)
  • .dirorder - order in which slicing directions are shown when switching through single-slice display
  • .fullsize - size of GUI when in full-size (read-only; side effects may occur when altered)
  • .fullsized - flag indicating whether GUI is in full-size mode (used by ne_swapfullsize)
  • .fullsizes - size information used to compute smaller UI size (read-only; side effects may occur when altered)
  • .gradient - flag indicating whether gradient display mode for current object is active (read-write)
  • .gradientu - flag indicating whether gradient display mode for underlay object is active (read-write)
  • .graylut - alternative gray-scale coloring scheme for lowest to highest color–i.e. can be used to inverse the display; read by ne_setslicepos (main UI slice display), ne_setsatslicepos (undocked slice display), ne_vismontage_ex (montage generation), ne_render_ex (slow, high-q rendering), and ne_render_setview (main UI based rendering); example: ne_gcfg.fcfg.graylut = flexinterpn(repmat([0,0,0;1,1,1], 3, 1), [inf, inf; 1, 1; 1/64, 1; 5-1/128, 3]);; for slice-based methods must be 256×3 in size, values between 0 and 255
  • .histpos - position of histogram and contrast/brightness selector of current object (read-only, side effects may occur when altered)
  • .histset - which limit of the histogram is to be set (0: auto-detect, 1: lower limit, 2: upper limit)
  • .histval - current range of histogram sliders (read-only, side effects may occur when altered)
  • .imethod - currently selected interpolation method (used by flexinterpn_method(DATA, COORD_RANGE, OPTIONS, IMETHOD)))
  • .join - join-stats mode flag
  • .joinmd2 - join-maximally-distance-colors mode for two stats maps flag
  • .joinulay - underlay-blending mode–if an Underlay object is selected, this is used by montagemix(OVERLAY, UNDERLAY, JOINULAY)
  • .localmax - search for local maxima in cluster tables
  • .localmaxsrf - search for local maxima in surface-based cluster tables
  • .localmaxsz - required minimum size for local maxima
  • .mods - cell array with key modifiers pressed (read-only)
  • .mpos - struct array keeping track of position and modifiers when mouse was pressed down to compute rotation and translation for slice, surface, and render displays
  • .nsynth - NeuroSynth-related configuration in fields .termm (available maps for re-loading) and .terms (available terms for loading via internet)
  • .noupdate - flag to instruct ne_setslicepos to not update the main UI (or perform any drawing operations)
  • .orient - neurological ('n') or radiological ('r') slice-based display (slice-only)
  • .page - current “page” (set of controls and axes objects) being displayed (read-only, use ne_showpage(PAGE) to select a different page; page 1: 3-slice view, page 2: single-slice view, page 3: surface view, and page 4: render view)
  • .paint - sub-structure with settings for the drawing/painting mode, set by ne_setdrawmode
    • .bbox - bounding-box for paint operation (read-only, no effect)
    • .code - intensity value (or color code) being written into the dataset when mode is 2 (2D painting) or 3 (3D painting)
    • .mode - painting mode, determines what action is performed by ne_setslicepos for drawing events; 1: browsing mode (no draw events), 2: 2D intensity-drawing (overwrite data with intensity/code, possibly blended), 3: 3D intensity-drawing (same), -2 and -3: 2D/3D undo-drawing (re-capture data from UndoBuffer)
    • .over - 1×2 range definition, execute drawing only over voxels within this range (incl. limits)
    • .rad - selected radius (read-only)
    • .shap2 - 2D shape for drawing (voxel selection)
    • .shap2w - 2D weighting vector (for smoothed drawing mode)
    • .shap3 - 3D shape for drawing
    • .shap3w - 3D weighting vector
    • .shape - kind of shape (read-only, 'b' square/box or 's' circle/sphere)
    • .smooth - smoothness indicator (read-only, between and including 0: no smoothness and 1: full smoothness)
    • .smootk - smoothness weights from kernel estimate (read-only)
  • .plp - current PLP object (used to fill the cluster-table text box with studies in close proximity to current position)
  • .prange - p-value range (multiplied with select p-threshold from dropdown control to compute upper statistical threshold)
  • .progress - unused struct
  • .renderer - selected Renderer property for main UI figure (read-only, side effects may occur when altered)
  • .sframe - slicing frame (bounding box, original and experimental feature, no longer reliably used; drawing does not work when altered)
  • .sframez - slicing frame (bounding box) when in “zoomed” mode (drawing does not work properly in this mode!)
  • .slicepos - position of slice view axes on UI (read-only, used to compute hit-tests, side effects may occur when altered)
  • .srfcfg - surface (and render) viewpoint configuration (read-only, can be altered with either ne_setsurfpos or ne_render_setview)
    • .anglex - azimuth angle
    • .angley - zenith angle
    • .time - sub-volume selector (only for MTC-based average surface time courses)
    • .trans - translation of surfaces/rendered volume
    • .zoom - zooming factor of surfaces/rendered volume
  • .stalphared - statistics-on-anatomical alpha-reduction factor (for rendering)
neuroelf_gui_-_global_config.txt · Last modified: 2014/06/04 19:46 by jochen