#SUMA ENVIRONMENT # If you do not have a ~/.sumarc file, cannot find a SUMA # environment variable that's been mentioned in documentation, # or fervently desire to update your current ~/.sumarc with # all the latest variables that SUMA uses, you should run: # # suma -update_env # # Unless you have setup SUMA environment variables outside of # your ~/.sumarc file, updating your ~/.sumarc file with # 'suma -update_env' WILL NOT ALTER changes you have already # made to the variables in your current ~/.sumarc. # For this reason consider running the update command after each # upgrade of your AFNI/SUMA binaries. ***ENVIRONMENT // 000-SUMA_ArrowRotAngle: // Incremental arrow rotation angle in degrees // default: SUMA_ArrowRotAngle = 5 SUMA_ArrowRotAngle = 5 // 001-SUMA_ColorPattern: // Color pattern (AFNI, EURO, DEFAULT) // default: SUMA_ColorPattern = EURO SUMA_ColorPattern = EURO // 002-SUMA_SwapButtons_1_3: // Swap mouse buttons 1 and 3 // default: SUMA_SwapButtons_1_3 = NO SUMA_SwapButtons_1_3 = NO // 003-SUMA_BackgroundColor: // Background color r g b. No space between values // default: SUMA_BackgroundColor = 0.0,0.0,0.0 SUMA_BackgroundColor = 0.0,0.0,0.0 // 004-SUMA_ROIColorMap: // ROI color map (bgyr64, roi64, roi128, roi256) // default: SUMA_ROIColorMap = ROI_i256 SUMA_ROIColorMap = ROI_i256 // 005-SUMA_NumConvSmooth: // Number of smoothing operations to run on convexity data // default: SUMA_NumConvSmooth = 5 SUMA_NumConvSmooth = 5 // 006-SUMA_ConvColorMap: // Colormap for convexity (gray02, gray_i02, ngray20, bgyr64, etc.) // default: SUMA_ConvColorMap = gray02 SUMA_ConvColorMap = gray02 // 007-SUMA_ConvBrightFactor: // Brightness factor for convexity // default: SUMA_ConvBrightFactor = 0.5 SUMA_ConvBrightFactor = 0.5 // 008-SUMA_NumForeSmoothing: // Number of smoothing operations to run on mixed foregroung color plane // before mixing with background // default: SUMA_NumForeSmoothing = 0 SUMA_NumForeSmoothing = 0 // 009-SUMA_NumFinalSmoothing: // Number of smoothing operations to run on final set of mixed colors. // This would be the mixed foreground and background colors // default: SUMA_NumFinalSmoothing = 0 SUMA_NumFinalSmoothing = 0 // 010-SUMA_ColorMixingMode: // Setup the color mixing mode (ORIG, MOD1) // default: SUMA_ColorMixingMode = ORIG SUMA_ColorMixingMode = ORIG // 011-SUMA_AFNI_TCP_PORT: // ** OBSOLETE: Port for communicating with AFNI // Listening ports are derived from SUMA_AFNI_TCP_PORT // Listening port i // SUMA_AFNI_TCP_PORT + i (i > 0) // default: SUMA_AFNI_TCP_PORT = 0 SUMA_AFNI_TCP_PORT = 0 // 012-SUMA_WarnBeforeClose: // Warn before closing with the Escape key (YES/NO) // default: SUMA_WarnBeforeClose = YES SUMA_WarnBeforeClose = YES // 013-SUMA_MaskZero: // Mask node values // 0 ? YES/NO // default: SUMA_MaskZero = YES SUMA_MaskZero = YES // 014-SUMA_AbsThreshold: // Threshold if Val < thr (NO) or | Val | < | Thr | (YES) // default: SUMA_AbsThreshold = YES SUMA_AbsThreshold = YES // 015-SUMA_ThresholdScalePower: // Threshold scale precision. 2 is the minimum allowed. // This value might be overridden in SUMA. // default: SUMA_ThresholdScalePower = 2 SUMA_ThresholdScalePower = 2 // 016-SUMA_CenterOnPatch: // Center of Rotation is based on nodes used in the mesh and not // on all the nodes in NodeList // default: SUMA_CenterOnPatch = NO SUMA_CenterOnPatch = NO // 017-SUMA_UseCrossTicks: // Use cross ticks on axis ? // default: SUMA_UseCrossTicks = NO SUMA_UseCrossTicks = NO // 018-SUMA_1D_Transpose_Warn: // Warn if 1D file looks like it needs a transpose // default: SUMA_1D_Transpose_Warn = YES SUMA_1D_Transpose_Warn = YES // 019-SUMA_AdjustMouseMotionWithZoom: // Adjust rotation and translation factor of mouse with changes // in zoom levels // default: SUMA_AdjustMouseMotionWithZoom = YES SUMA_AdjustMouseMotionWithZoom = YES // 020-SUMA_ViewOrthographicProjection: // Use orthographic projection // default: SUMA_ViewOrthographicProjection = NO SUMA_ViewOrthographicProjection = NO // 021-SUMA_KeyZoomGain: // Percent gain for zooming in and out with the 'z' and 'Z' keys. // Typical range from 0 to 50 // default: SUMA_KeyZoomGain = 5 SUMA_KeyZoomGain = 5 // 022-SUMA_FOV_Original: // Original FOV. Set between 1.0 and 100.0 // Default is 30.0, -1 == auto // default: SUMA_FOV_Original = -1 SUMA_FOV_Original = -1 // 023-SUMA_Position_Original: // Original windows size and width in pixels // Allowed values are: 'TopLeft' // 'RightOffset' // 'X Y' Sets only the position to top left corner // 'X Y Xwidth Ywidth' Set also width of window // Default is top left of the screen // default: SUMA_Position_Original = TopLeft SUMA_Position_Original = TopLeft // 024-SUMA_Light0Color: // light0 color // default: SUMA_Light0Color = 1.0,1.0,1.0 SUMA_Light0Color = 1.0,1.0,1.0 // 025-SUMA_AmbientLight: // Ambient light // default: SUMA_AmbientLight = 1.0,1.0,1.0 SUMA_AmbientLight = 1.0,1.0,1.0 // 026-SUMA_AllowDsetReplacement: // Allow for replacement of pre-loaded dsets // default: SUMA_AllowDsetReplacement = YES SUMA_AllowDsetReplacement = YES // 027-SUMA_AlwaysAssignSurface: // Allow a dataset to be assigned to a surface, even if // domain of dset is specified and different for the surface. // Default is yes // default: SUMA_AlwaysAssignSurface = YES SUMA_AlwaysAssignSurface = YES // 028-SUMA_ShareGrandChildrenOverlays: // Allow for surfaces with same DomainGrandParentID to share overlays // default: SUMA_ShareGrandChildrenOverlays = NO SUMA_ShareGrandChildrenOverlays = NO // 029-SUMA_SnapshotOverSampling: // Increase the resolution of images recorded with 'r' button. // Increase is done by taking multiple shots that once stitched // together form a high-resolution image. // The maximum resolution is set by the GL_MAX_VIEWPORT_DIMS of your // graphics card. I have 4096 pixels. // If you exceed this number, SUMA will make adjustments automatically. // Assemble images with program 2dcat. // default: SUMA_SnapshotOverSampling = 1 SUMA_SnapshotOverSampling = 1 // 030-SUMA_NoDuplicatesInRecorder: // Ignore consecutive duplicate images in recorder // default: SUMA_NoDuplicatesInRecorder = YES SUMA_NoDuplicatesInRecorder = YES // 031-SUMA_START_NIML: // start NIML (can't do this for more than one suma at a time!) // default: SUMA_START_NIML = YES SUMA_START_NIML = YES // 032-SUMA_AllowFilenameDsetMatch: // Allow (YES) datasets with the same filename but differing ID // to be considered the same. // This is only useful with SUMA_AllowDsetReplacement // default: SUMA_AllowFilenameDsetMatch = YES SUMA_AllowFilenameDsetMatch = YES // 033-SUMA_FreezeFOVAcrossStates: // Freeze zoom across states // default: SUMA_FreezeFOVAcrossStates = NO SUMA_FreezeFOVAcrossStates = NO // 034-SUMA_DsetColorMap: // Dset color map // default: SUMA_DsetColorMap = Spectrum:red_to_blue SUMA_DsetColorMap = Spectrum:red_to_blue // 035-SUMA_ShowOneOnly: // Show only selected dset in suma's surface controller. // default: SUMA_ShowOneOnly = YES SUMA_ShowOneOnly = YES // 036-SUMA_GraphHidden: // Update graphs, even SUMA_ShowOneOnly (or suma's '1 Only') is turned on. // default: SUMA_GraphHidden = YES SUMA_GraphHidden = YES // 037-SUMA_ColorMapRotationFraction: // Fraction of colormap to rotate with up/down arrow keys. // default: SUMA_ColorMapRotationFraction = 0.05 SUMA_ColorMapRotationFraction = 0.05 // 038-SUMA_SurfContFontSize: // Size of surface controller font. // Values are SMALL, BIG (old style). // default: SUMA_SurfContFontSize = SMALL SUMA_SurfContFontSize = SMALL // 039-SUMA_StartUpLocation: // Where to position SUMA window when first opened. // Values are POINTER (at the mouse pointer's location) // DEFAULT (let the window manager decide) // // default: SUMA_StartUpLocation = DEFAULT SUMA_StartUpLocation = DEFAULT // 040-SUMA_KeyNodeJump: // Numer of nodes to jump with the 'alt+arrow' keys. // Valid range from 1 to 10 // default: SUMA_KeyNodeJump = 1 SUMA_KeyNodeJump = 1 // 041-SUMA_DriveSumaMaxWait: // Numer of seconds to wait for SUMA to respond to DriveSuma. // Valid range from 0 to 60000 // default: SUMA_DriveSumaMaxWait = 300.0 SUMA_DriveSumaMaxWait = 300.0 // 042-SUMA_LEFT_FILE_DSET_IDENTIFIER: // String to use in creating left hemisphere dataset wildcards. // default: SUMA_LEFT_FILE_DSET_IDENTIFIER = *lh*.dset SUMA_LEFT_FILE_DSET_IDENTIFIER = *lh*.dset // 043-SUMA_RIGHT_FILE_DSET_IDENTIFIER: // String to use in creating left hemisphere dataset wildcards. // default: SUMA_RIGHT_FILE_DSET_IDENTIFIER = *rh*.dset SUMA_RIGHT_FILE_DSET_IDENTIFIER = *rh*.dset // 044-SUMA_LEFT_FILE_ROI_IDENTIFIER: // String to use in creating left hemisphere roi wildcards. // default: SUMA_LEFT_FILE_ROI_IDENTIFIER = *lh*.roi SUMA_LEFT_FILE_ROI_IDENTIFIER = *lh*.roi // 045-SUMA_RIGHT_FILE_ROI_IDENTIFIER: // String to use in creating right hemisphere roi wildcards. // default: SUMA_RIGHT_FILE_ROI_IDENTIFIER = *rh*.roi SUMA_RIGHT_FILE_ROI_IDENTIFIER = *rh*.roi // 046-SUMA_LEFT_FILE_OTHER_IDENTIFIER: // String to use in creating left hemisphere roi wildcards. // default: SUMA_LEFT_FILE_OTHER_IDENTIFIER = *lh* SUMA_LEFT_FILE_OTHER_IDENTIFIER = *lh* // 047-SUMA_RIGHT_FILE_OTHER_IDENTIFIER: // String to use in creating right hemisphere roi wildcards. // default: SUMA_RIGHT_FILE_OTHER_IDENTIFIER = *rh* SUMA_RIGHT_FILE_OTHER_IDENTIFIER = *rh* // 048-SUMA_ConvexityDsetOpacity: // Initial Convexity Datasest opacity. // default: SUMA_ConvexityDsetOpacity = 0.85 SUMA_ConvexityDsetOpacity = 0.85 // 049-SUMA_ShowLabelDsetAtStartup: // Display mode of Label Datasest specified in spec file at startup. // 'YES' or 'Col': Shows it in color // 'Con': Shows only contours (see also env SUMA_ContourThickness). // 'C&C': Shows both colors and contours // 'XXX'or 'No': Does not show it. // // default: SUMA_ShowLabelDsetAtStartup = XXX SUMA_ShowLabelDsetAtStartup = XXX // 050-SUMA_ShowLabelsAtCrossHair: // Show label at cross hair in viewer // You can toggle the display at such labels with F9 // // default: SUMA_ShowLabelsAtCrossHair = YES SUMA_ShowLabelsAtCrossHair = YES // 051-SUMA_LabelDsetOpacity: // Initial Label Datasest opacity. // default: SUMA_LabelDsetOpacity = 0.2 SUMA_LabelDsetOpacity = 0.2 // 052-SUMA_AttemptTalkRecover: // Attempt to recover from AFNI <--> SUMA disconnection bug. // // default: SUMA_AttemptTalkRecover = Yes SUMA_AttemptTalkRecover = Yes // 053-SUMA_CmapsDir: // Name of directory containing user's own SUMA color maps (*.cmap) // // default: SUMA_CmapsDir = None SUMA_CmapsDir = ~/suma_colormaps // 054-SUMA_RetinoAngle_DsetColorMap: // Name of color map for datasets of retinotopy angles. // These would be produced by 3dRetinoPhase // // default: SUMA_RetinoAngle_DsetColorMap = rgybr20 SUMA_RetinoAngle_DsetColorMap = rgybr20 // 055-SUMA_VFR_DsetColorMap: // Name of color map for VFR datasets produced by SurfRetinoMap // // default: SUMA_VFR_DsetColorMap = afni_n2 SUMA_VFR_DsetColorMap = afni_n2 // 056-SUMA_NodeCoordsUnits: // Coordinate units of surface nodes. Choose from 'mm' or 'cm' // A bad choice can make the surfaces render with many artifacts. // // default: SUMA_NodeCoordsUnits = mm SUMA_NodeCoordsUnits = mm // 057-SUMA_DoNotSendStates: // Which anatomically correct surf. states should not NOT be sent to AFNI? // This is mostly for deciding whether one of 'white' or 'smoothwm' // FreeSurfer states should not be sent to AFNI. // The default is to let them all go. // You can specify multiple states with a , delimited list (no spaces!). // By default nothing is excluded. // // default: SUMA_DoNotSendStates = N/A SUMA_DoNotSendStates = N/A // 058-SUMA_AutoRecordPrefix: // Prefix for autorecord (suma's Ctrl+R) files. // FreeSurfer states should not be sent to AFNI. // Add a path if you want the files to endup in a particular directory. // You can also add an extension to prefix to specify the output type. // Choose from .jpg, .ppm, or .1D . The fallback type is .jpg // // default: SUMA_AutoRecordPrefix = ./SUMA_Recordings/autorecord.jpg SUMA_AutoRecordPrefix = ./SUMA_Recordings/autorecord.jpg // 059-SUMA_CrossHairLabelFont: // Font for cross hair label in SUMA viewer // Choose one of: f8 f9 tr10 tr24 he10 he12 he18 // // default: SUMA_CrossHairLabelFont = f9 SUMA_CrossHairLabelFont = f9 // 060-SUMA_IxT_LinkMode: // Linking mode of I and T sub-brick selectors // Choose one of: None, Same, Stat // // default: SUMA_IxT_LinkMode = Stat SUMA_IxT_LinkMode = Stat // 061-SUMA_ArrowFieldSelectorTrigger: // Minimum Number of sub-bricks to trigger use of arrow field for // sub-brick selectors. // // default: SUMA_ArrowFieldSelectorTrigger = 200 SUMA_ArrowFieldSelectorTrigger = 50 // 062-SUMA_Sym_I_Range: // Use symmetric Intensity range by default (YES or NO) // // default: SUMA_Sym_I_Range = YES SUMA_Sym_I_Range = YES // 063-SUMA_Auto_I_Range: // Set auto Intensity range by default (YES or NO) // // default: SUMA_Auto_I_Range = NO SUMA_Auto_I_Range = NO // 064-SUMA_Auto_B_Range: // Set auto Brightness range by default (YES or NO) // // default: SUMA_Auto_B_Range = NO SUMA_Auto_B_Range = NO // 065-SUMA_ContourThickness: // Set thickness of dataset contours // // default: SUMA_ContourThickness = 1.0 SUMA_ContourThickness = 1.0 // 066-SUMA_LHunify: // Merge separated left/right states for inflated/spherical/etc. surfaces // Choose from YES or NO // default: SUMA_LHunify = YES SUMA_LHunify = YES