AFNI file: AFNI.afnirc
// This is a sample .afnirc file.
// Copy it into your home directory, with the name '.afnirc'.
// Then edit it to your heart's delight.
// See README.setup and README.environment for documentation.
***COLORS
// Define new overlay colors. These will appear on the color menus.
salmon = #ff8866
navy = navyblue
***ENVIRONMENT
// Most (not all) of the Unix environment variables that affect AFNI
IDCODE_PREFIX = AFN // 3 letter prefix for dataset ID codes
// AFNI_graph_boxes_thick = 0 // 0=thin lines, 1=thick lines, for graph boxes
// AFNI_graph_grid_thick = 0 // ditto for the graph vertical grid lines
AFNI_graph_data_thick = 1 // ditto for the data graphs
AFNI_graph_ideal_thick = 1 // ditto for the ideal graphs
AFNI_graph_ort_thick = 1 // ditto for the ort graphs
AFNI_graph_dplot_thick = 1 // ditto for the dplot graphs
AFNI_graph_ggap = 3 // initial spacing between graph boxes
AFNI_graph_width = 512 // initial width of graph window
AFNI_graph_height = 384 // initial height of graph window
// AFNI_graph_matrix = 3 // initial number of sub-graphs
AFNI_GRAPH_TEXTLIMIT = 20 // max number of rows shown in Graph popup
// AFNI_GRAPH_BASELINE = Individual // type of baseline to set in Graph windows
// AFNI_GRAPH_GLOBALBASE = 0 // value for Global baselines in Graph windows
// AFNI_montage_periodic = True // allows periodic montage wraparound
// AFNI_purge = True // allows automatic dataset memory purge
// AFNI_resam_vox = 1.0 // dimension of voxel (mm) for resampled datasets
// AFNI_resam_anat = Li // One of NN, Li, Cu, Bk for Anat resampling mode
// AFNI_resam_func = NN // ditto for Func resampling mode
// AFNI_resam_thr = NN // for Threshold resampling mode
// AFNI_pbar_posfunc = True // will start color pbar as all positive
// AFNI_pbar_sgn_pane_count = 8 // # of panes to start signed color pbar with
// AFNI_pbar_pos_pane_count = 8 // # of panes to start positive color pbar with
// AFNI_pbar_hide = True // hide color pbar when it is being altered
// AFNI_PBAR_IMXY = 200x20 // size of saved pbar color image
// AFNI_PBAR_LOCK = YES // lock color pbars together
// AFNI_OVERLAY_ZERO = NO // YES==colorize zero values in Overlay dataset
// AFNI_THRESH_LOCK = YES // lock threshold sliders together
// AFNI_THRESH_AUTO = YES // YES==AFNI guesses a threshold
// AFNI_SLAVE_FUNCTIME = NO // YES==time index changes overlay AND underlay
// AFNI_SLAVE_THRTIME = NO // YES==time index changes threshold, too
// AFNI_COLORSCALE_DEFAULT = Spectrum:red_to_blue // initial colorscale for pbar
// AFNI_chooser_listmax = 20 // max items in a chooser before scrollbars appear
// AFNI_MAX_OPTMENU = 999 // max # items in an 'option menu'
// AFNI_DONT_MOVE_MENUS = YES // don't try to move popup menu windows
// AFNI_MENU_COLSIZE = 30 // max number of entries in a popup menu column
// AFNI_DISABLE_TEAROFF = NO // YES==disable the menu 'tearoff' capability
// AFNI_DONT_SORT_ENVIRONMENT = NO // YES==disable sorting Edit Environment
// AFNI_ORIENT = RAI // coordinate order
// AFNI_NOPLUGINS = NO // YES==disable plugins
// AFNI_YESPLUGOUTS = NO // YES==enable plugouts (POs)
// AFNI_PLUGOUT_TCP_BASE = 6666 // overrides default TCP/IP socket for plugouts
// AFNI_PLUGINPATH = /home/rwcox/abin // directory for plugins
// AFNI_TSPATH = /home/rwcox/stuff // directory for .1D files
// AFNI_MODELPATH = /home/rwcox/abin // directory for NLfim models
// TMPDIR = /tmp // directory for temporary files
// AFNI_GLOBAL_SESSION = /data/junk // directory w/datasets you always see
// AFNI_BYTEORDER = LSB_FIRST // to force .BRIK byte order on output
// AFNI_BYTEORDER_INPUT = LSB_FIRST // when .HEAD file fails to specify
// AFNI_NO_BYTEORDER_WARNING = YES // do NOT print out byte-ordering warning
AFNI_SESSTRAIL = 1 // # of directory levels to show in filenames
AFNI_HINTS = YES // YES==turns on popup hints
// AFNI_COMPRESSOR = gzip // force all .BRIK output to be compressed
AFNI_AUTOGZIP = YES // gzip .BRIK files if it's a good idea
// AFNI_NOMMAP = YES // to disable use of mmap() file I/O
AFNI_LEFT_IS_LEFT = YES // YES==show human left on screen left
// AFNI_ENFORCE_ASPECT = YES // AFNI to enforce image aspect ratio
AFNI_ALWAYS_LOCK = YES // to start with all AFNI controllers locked
// AFNI_NOREALPATH = NO // don't convert filenames to 'real' names
// AFNI_NO_MCW_MALLOC = NO // YES==turn off debugging malloc use
AFNI_FLOATSCAN = YES // YES==scan float datasets for errors
// AFNI_NOSPLASH = NO // YES==turn off the AFNI splash window
AFNI_SPLASH_XY = 444:222 // x:y coordinates for splash window
// AFNI_SPLASHTIME = 3 // how many seconds splash window stays up
// AFNI_NOTES_DLINES = 11 // # of text entry lines in the Notes plugin
// AFNI_MARKERS_NOQUAL = NO // YES==AFNI won't do 'quality' for markers
AFNI_NO_ADOPTION_WARNING = YES // YES==AFNI won't show dataset 'adoption' warnings
AFNI_VIEW_ANAT_BRICK = YES // try to view data without warp-on-demand
AFNI_VIEW_FUNC_BRICK = YES // try to view data without warp-on-demand
AFNI_tsplotgeom = 512x384 // size of time series plot windows
AFNI_PLUGINS_ALPHABETIZE = YES // whether to alphabetize Plugins menu
// AFNI_VOLREG_EDGING = 5 // size of edge region to mask out in 3dvolreg
// AFNI_ROTA_ZPAD = 5 // size of zero padding to use in 3dvolreg
AFNI_ncolors = 80 // number of gray levels to use in underlay
AFNI_gamma = 1.7 // gamma correction for underlay intensities
AFNI_GRAYSCALE_BOT = 25 // minimum image intensity graylevel (0-255)
AFNI_IMAGE_MINFRAC = 0.04 // minimum size of AFNI image window
AFNI_IMAGE_MAXFRAC = 0.88 // maximum size of AFNI image window
// AFNI_IMAGE_MINTOMAX = NO // YES=start Image window in Min-to-Max mode
// AFNI_IMAGE_CLIPPED = NO // YES=start Image window in Clipped mode
// AFNI_IMAGE_CLIPBOT = 0.25 // bottom level scaling for Clipped mode
// AFNI_IMAGE_CLIPTOP = 1.0 // top level scaling for Clipped mode
// AFNI_IMAGE_GLOBALRANGE = NO // YES=scale Image grayleves in 3D
AFNI_KEEP_PANNING = YES // keep Pan mode turned on in Image windows
// AFNI_IMAGE_LABEL_MODE = 1 // draw labels in upper left of Image windows
// AFNI_IMAGE_LABEL_SIZE = 2 // size of labels in Image windows
// AFNI_IMAGE_LABEL_COLOR = white // color of labels in Image windows
// AFNI_IMAGE_LABEL_SETBACK = 0.01 // distance from edges for labels
// AFNI_CROSSHAIR_LINES = YES // draw crosshairs with lines, not voxels
// AFNI_CROP_ZOOMSAVE = NO // how to save zoomed Image windows
// AFNI_IMAGE_ZEROCOLOR = white // color to show for 0 voxels in Image window
// AFNI_IMAGE_ENTROPY = 0.2 // image entropy at which to disable 2%-to-98%
// AFNI_IMAGE_ZOOM_NN = NO // YES==don't linearly interpolate zoomed images
// AFNI_IMAGE_SAVESQUARE = NO // YES==always save images with square pixels
// AFNI_IMAGE_TICK_DIV_IN_MM = NO // YES==image tick mark spacings are in mm
// AFNI_IMAGRA_CLOSER = NO // YES==Image/Graph button second clicks closes
AFNI_DEFAULT_OPACITY = 8 // default opacity level for Image windows
AFNI_DEFAULT_IMSAVE = jpg // default Image window Save format
// AFNI_OLD_PPMTOBMP = NO // YES==color quantize BMP output images
AFNI_VIDEO_DELAY = 66 // ms between 'v' key image cycling
// AFNI_STROKE_THRESHOLD = 8 // min mouse movement for grayscale edit
// AFNI_STROKE_AUTOPLOT = YES // YES=show grayscale histogram in edit
// AFNI_NO_SIDES_LABELS = NO // YES==AFNI won't show 'left=Left' labels
// AFNI_MINC_DATASETS = YES // try to read .mnc files as datasets
// AFNI_MINC_FLOATIZE = YES // convert .mnc files to floats on input
// AFNI_MINC_SLICESCALE = YES // scale each .mnc slice separately
// AFNI_ANALYZE_DATASETS = YES // read ANALYZE-7.5 files as datasets
// AFNI_ANALYZE_FLOATIZE = YES // convert ANALYZE data to floats on input
// AFNI_ANALYZE_SCALE = YES // use the 'funused1' value for scaling
// AFNI_ANALYZE_ORIGINATOR = YES // use the SPM ORIGINATOR field
// AFNI_ANALYZE_ORIENT = LPI // orientation for ANALYZE datasets
// AFNI_ANALYZE_AUTOCENTER = NO // make center of file have (x,y,z)=(0,0,0)?
// AFNI_MPEG_DATASETS = NO // YES==try to read .mpg files as datasets
// AFNI_MPEG_GRAYIZE = NO // YES==convert .mpg datasets to grayscale
// AFNI_START_SMALL = NO // set initial AFNI dataset to smallest one
AFNI_DISP_SCROLLBARS = YES // YES==show scrollbars on Disp panel
// AFNI_VALUE_LABEL = YES // show data value label in Define Overlay
// AFNI_SUMA_LINECOLOR = blue // color for surface lines from SUMA
// AFNI_SUMA_LINESIZE = 2 // thickness of lines from SUMA
// AFNI_SUMA_BOXSIZE = 3 // size of node boxes from SUMA
// AFNI_SUMA_BOXCOLOR = yellow // color for node boxes from SUMA
// AFNI_SHOW_SURF_POPUPS = NO // YES==see info windows from SUMA data transfers
// AFNI_KILL_SURF_POPUPS = NO // YES==don't see any info from SUMA data xfers
// AFNI_LOAD_PRINTSIZE = 100M // print warning that large file is being loaded
// AFNI_VERSION_CHECK = YES // NO==disable weekly version check over Web
// AFNI_MOTD_CHECK = YES // NO==disable display of Message-of-the-Day
// AFNI_AGIF_DELAY = 10 // centi-seconds between animated GIF frames
// AFNI_MPEG_FRAMERATE = 24 // MPEG-1 frame rate for saved movies
// AFNI_SLICE_SPACING_IS_GAP = NO // YES==fix GE DICOM error
// AFNI_DICOM_RESCALE = NO // YES==use DICOM rescale tags
// AFNI_DICOM_WINDOW = NO // YES==use DICOM window tags
// AFNI_RESCAN_METHOD = Add // add new datasets, don't replace old ones
// AFNI_STARTUP_WARNINGS = YES // NO==turn off some warning message at startup
// AFNI_1D_TIME = NO // YES==.1D files columns are the time axis
// AFNI_1D_TIME_TR = 1.0 // value for TR of a .1D time file
// AFNI_3D_BINARY = YES // YES==save .3D files in binary format
// AFNI_DRAW_UNDOSIZE = 4 // # Mbytes for Draw Dataset undo buffer
// AFNI_DISABLE_CURSORS = NO // YES==don't try to change X11 cursors
// AFNI_CLICK_MESSAGE = NO // YES==see stupid 'click here to pop down' message
// AFNI_X11_REDECORATE = YES // NO==don't try to change X11 window controls
// AFNI_MAX_1DSIZE = 66666 // max size of .1D files to automatically read
// AFNI_TITLE_LABEL2 = NO // YES==use dataset 'label2' field in titlebar
// AFNI_EDGIZE_OVERLAY = NO // YES==show only edges of color overlay blobs
// AFNI_DONT_LOGFILE = NO // YES==don't log AFNI programs to ~/.afni.log
// AFNI_WRITE_NIML = NO // YES==write .HEAD files in NIML format
// AFNI_TTATLAS_CAUTION = YES // NO==disable warning message in 'wherami'
// AFNI_RESCAN_AT_SWITCH = YES // YES==rescan directory for new datasets
// AFNI_DATASET_BROWSE = YES // YES==dataset item selection acts immediately
// AFNI_OVERLAY_ONTOP = YES // YES==put 'Overlay' button above 'Underlay'
// AFNI_NIML_START = YES // start NIML listening when AFNI starts
// NIML_TRUSTHOST_01 = 192.168.0.1 // IP address of host to trust for NIML
AFNI_plug_drawdset_butcolor = #992066 // For the Plugins menu.
// AFNI_plug_histog_butcolor = #663199 // Colors are drawn from
AFNI_plug_crender_butcolor = #cc1033 // the RBGCYC map in afni.h
// AFNI_hotcolor = navyblue // color for 'Done', 'Set', etc.
// AFNI_NO_NEGATIVES_WARNING = NO // YES==to3d won't warn about negative values
// AFNI_TO3D_ZPAD = 0 // # of zero padding slices to add in to3d
// AFNI_TRY_DICOM_LAST = NO // YES==DICOM is last image format tried in to3d
// AFNI_ALLOW_MILLISECONDS = NO // YES==allow 'ms' time units in to3d
// AFNI_STARTUP_SCRIPT = /home/rwcox/.afni_script // script to run at AFNI start
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Fri Jan 30 20:02:53 EST 2009