issue loading standard MNI images in AFNI

[GiriKrish]

Hi Keith, Bruce and I noticed that standard MNI images (1 and 2mm) are not loading correctly in AFNI. The sign on y co-ordinate is flipped such that actual posterior parts of the brain is indexed as frontal parts of the brain, and vice versa. However, when we check the same (x,y,z) co-ordinate in fsleyes, we don't have this issue. I am guessing that this issue may have something to do with AFNI environment setup. Could you please help with this ?

We saw this issue working from lens...not sure about other computers/nodes.

Thanks, Giri.

[kmcgregor123456]

I think this is an RAI->LPI issue. AFNI defaults to RAI but can be changed to the more neuroimaging standard LPI (FSL Standard). We might as well just go ahead and change that to do so, since we use the two environments interchangably.

I created an .afnirc file for your account and placed it in your home directory. This file sets up the environment to default to LPI instead of RAI.

Log in again and check if the error exists:

// 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_SPLASH_MELT = NO // whether to use the 'melt' effect

// 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

AFNI_ONE_OBLIQUE_WARNING = YES // In AFNI interface, mention oblique warnings just once

AFNI_GRAPH_FORCE_AUTO_SCALE = YES // Autoscale graphs each time they are redrawn

[GiriKrish]

Thanks for creating the .afnirc file and placing it my home directory Keith. Actually, we encountered this issue under Anna’s login when Bruce and I were helping with her results. In one of the research group meetings, if you don’t mind teaching us how to change environment variables (and other general stuff that we can do on our own), that will save your time from bunch of us bugging you with these issues. ☺

Best, Giri.

From: Keith McGregor [mailto:notifications@github.com] Sent: Friday, August 24, 2018 6:26 PM To: kmcgregor123456/CVNRimagingCore Cc: Krishnamurthy, Venkatagiri; Author Subject: Re: [kmcgregor123456/CVNRimagingCore] issue loading standard MNI images in AFNI (#52)

I think this is an RAI->LPI issue. AFNI defaults to RAI but can be changed to the more neuroimaging standard LPI (FSL Standard). We might as well just go ahead and change that to do so, since we use the two environments interchangably.

I created an .afnirc file for your account and placed it in your home directory. This file sets up the environment to default to LPI instead of RAI.

Log in again and check if the error exists:

// 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_SPLASH_MELT = NO // whether to use the 'melt' effect

// 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

AFNI_ONE_OBLIQUE_WARNING = YES // In AFNI interface, mention oblique warnings just once

AFNI_GRAPH_FORCE_AUTO_SCALE = YES // Autoscale graphs each time they are redrawn

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