NeuroElf wiki

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====== NeuroElf - global configuration (variable) ======

===== Motivation =====
For the purpose of keeping a globally accessible configuration, a single 1x1 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 1x1 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) ===
  * **''.CM''** - contrast manager configuration (to execute [[glm.FFX_tMap|GLM::FFX_tMap]], [[glm.RFX_rMap|GLM::RFX_rMap]], and [[glm.RFX_tMap|::RFX_tMap]])
  * **''.MDM''** - multi-study design matrix dialog (to configure and create a GLM with [[mdm.ComputeGLM|MDM::ComputeGLM]])
  * **''.MKDA''** - MKDA interface (configuring and then executing [[plp.MKDA|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.

=== 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 ''[[vmp.ClusterTable|OBJ::ClusterTable]](MAP_NUMBER, MAP_THRESHOLD, struct('clconn', **CLCONN**, ...))'')
  * **''.clim''** - cluster-restriction limitation (for ''[[voi.Combine|VOI::Combine]](LIST_OF_VOIS, 'restrict', struct('rsize', **CLIM**, ...))'')
  * **''.clsort''** - cluster-sorting algorithm (for ''[[vmp.ClusterTable|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 256x3 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''** - 1x2 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)
  *