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).
.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).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)