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

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)

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).

• .CM - contrast manager configuration (to execute GLM::FFX_tMap, GLM::RFX_rMap, and ::RFX_tMap)
• .MDM - multi-study design matrix dialog (to configure and create a GLM with MDM::ComputeGLM)
• .MKDA - MKDA interface (configuring and then executing PLP::MKDA)
• .RM - RFX- (single-level) mediation dialog (to execute mediationpset and store results in a VMP)
• .Render - Render dialog (feeding ne_render_setview and ne_render_ex)
• .VisMontage - montage dialog (feeding ne_vismontage_ex)

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

• .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)