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neuroelf_gui_-_global_config [2014/06/04 17:08]
jochen created
neuroelf_gui_-_global_config [2014/06/04 19:46]
jochen
Line 18: Line 18:
  
 ==== Figure-based configuration ==== ==== Figure-based configuration ====
-The subfield ''​ne_gcfg.fcfg''​ contains the following ​fields:+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) === === Fixed child-dialogs (single instance allowed per dialog) ===
-  * **''​.CM''​** - contrast manager configuration (to execute GLM::​FFX_tMap,​ GLM::​RFX_rMap,​ and GLM::​RFX_tMap) +  * **''​.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''​** - 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) +  * **''​.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) +  * **''​.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) +  * **''​.Render''​** - Render dialog (feeding ​[[ne_render_setview]] and [[ne_render_ex]]
-  * **''​.VisMontage''​** - montage dialog (feeding ne_vismontage_ex)+  * **''​.VisMontage''​** - montage dialog (feeding ​[[ne_vismontage_ex]])
 These dialogs'​ configurations are described in greater detail on their own pages. 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)
 +  * 
neuroelf_gui_-_global_config.txt · Last modified: 2014/06/04 19:46 by jochen