1 static char * readme_afnigui[] = { 2 "================================================================================\n" , 3 " ----===| Usage Tips for the AFNI GUI |===----\n" , 4 "================================================================================\n" , 5 "Tip #1:\n" , 6 " When the AFNI sunrise logo is displayed in the square to right of the 'done'\n" , 7 " button, this means that something is happening that might take a long time\n" , 8 " (e.g., reading a big file). The AFNI GUI will not respond to clicks or\n" , 9 " keystrokes during this time.\n" , 10 "--------------------------------------------------------------------------------\n" , 11 " ***** AFNI For Absolute Beginners *****\n" , 12 "\n" , 13 "(1) To use AFNI, you must have some data stored in a format that the program\n" , 14 " understands.\n" , 15 " (a) The major formats for which AFNI is programmed are:\n" , 16 " ++ AFNI formatted datasets, in .HEAD and .BRIK pairs of files;\n" , 17 " ++ NIfTI-1 formatted datasets, in .nii or .nii.gz files.\n" , 18 " (b) When you start AFNI, any datasets in the current directory will be ready\n" , 19 " for viewing. If there are no datasets to read, AFNI will pop up a\n" , 20 " message. At this point, you can do one of 2 things:\n" , 21 " ++ Quit AFNI, change directory ('cd') to a directory with some datasets,\n" , 22 " and restart the program (this is what I always do); or,\n" , 23 " ++ Use the 'DataDir Read' button in the second column of the main AFNI\n" , 24 " controller to navigate to a directory with some datasets.\n" , 25 " When there is no data, AFNI creates a 'dummy' dataset for you to look at,\n" , 26 " if you want to play with the image viewers.\n" , 27 " (c) To open an image viewer, click on one of the 'Image' buttons in the left\n" , 28 " column of the main AFNI controller.\n" , 29 " ++ Left-click in the image to move the crosshairs around.\n" , 30 " ++ Click or click-drag in the slider below the image to change slice.\n" , 31 " ++ The controls to the right of the image let you adjust the image\n" , 32 " contrast, brightness, zoom factor, etc.\n" , 33 " ++ The controls to the bottom of the image let you carry out various\n" , 34 " operations on the image, such as saving to JPEG format, and making\n" , 35 " a montage (array) of slice images.\n" , 36 " (d) If a dataset has more than one 3D volume in it (usually that means it\n" , 37 " has a time axis, like an FMRI EPI dataset), then you can use the 'Graph'\n" , 38 " buttons to view an array of graphs of the voxel data time series.\n" , 39 " ++ The crosshairs in the image viewer that corresponds to the graph\n" , 40 " viewer change to a small box to indicate which voxels are the source\n" , 41 " of the data in the graph array.\n" , 42 " (e) The viewpoint of multiple image and graph viewers (the focus voxel at the\n" , 43 " crosshairs) is always locked together -- Left-click in one image to move\n" , 44 " the crosshairs, and all other open image and graph viewers will jump, too.\n" , 45 " ++ Moving the time index in a graph viewer (by clicking in the central\n" , 46 " sub-graph, or by using the 'Index' control in the main AFNI window)\n" , 47 " will cause all the image and graph viewers to display at the new\n" , 48 " time index.\n" , 49 " (f) At any moment, you can have one underlay dataset (grayscale) and one\n" , 50 " overlay dataset (color). To choose which datasets are visible, use\n" , 51 " the 'UnderLay' and 'OverLay' button in the second column of the AFNI\n" , 52 " controller.\n" , 53 " ++ To control whether the color overlay is visible, click on the \n" , 54 " 'See OverLay' toggle button.\n" , 55 " ++ To manage how the numbers in the overlay dataset are converted into\n" , 56 " colors, click on 'Define OverLay' to open up a new control panel.\n" , 57 " ++ The active underlay and overlay dataset names are shown in the title\n" , 58 " bar of the AFNI controller window.\n" , 59 " (g) Don't be afraid of the software! The popup hints will help. The button\n" , 60 " 'BHelp' will give you longer help about individual buttons -- click on\n" , 61 " the BHelp button, then click on any AFNI button to get a small text box\n" , 62 " with more help than the simple popup hints.\n" , 63 " (h) Sample datasets and all the AFNI course materials are in the big file\n" , 64 " CD.tgz (more than 1 Gbyte) at\n" , 65 " https://afni.nimh.nih.gov/pub/dist/edu/data\n" , 66 " And don't forget the AFNI message board at\n" , 67 " https://afni.nimh.nih.gov/afni/community/board\n" , 68 "--------------------------------------------------------------------------------\n" , 69 " ***** Cursor Shapes and Right-Click Popup Menus *****\n" , 70 "\n" , 71 "(2) On most systems, the X11 cursor used in AFNI is an orange arrow pointing\n" , 72 " at about '10:30' on the clock face. However, the arrow becomes yellow\n" , 73 " and points more steeply, to about '11:00', when it is over a location that\n" , 74 " has a hidden Right-Click popup menu. Some of these are:\n" , 75 " (a) Over the logo square just to the right of the 'done' button in an\n" , 76 " AFNI controller.\n" , 77 " (b) Over the labels at the top of the threshold slider and color bar in\n" , 78 " the 'Define Overlay' control panel.\n" , 79 " (c) On the label to the left of a drop-down 'option menu'; e.g., 'Xhairs'\n" , 80 " or 'ULay' (for these menus, the cursor will not change shape).\n" , 81 " (d) Over the color bar itself, when it is in continuous 'colorscale' mode\n" , 82 " ('**') -- but not when it is in discrete color panel mode.\n" , 83 " (e) Over the image viewer main sub-window, which holds the image itself.\n" , 84 " (f) Over the image viewer intensity bar, just to the right of the image.\n" , 85 " (g) Over the 'Save' button in the image viewer.\n" , 86 " (h) Over the 'crop' button in the image viewer.\n" , 87 " (i) Over the sub-graphs in the time series dataset graph viewer\n" , 88 " (pops up some statistics about the data in the sub-graph).\n" , 89 " (j) Over the coordinate display in the upper left corner of an AFNI\n" , 90 " controller.\n" , 91 " (k) In the 'Render Dataset' plugin, over the 'See Xhairs' and 'Accumulate'\n" , 92 " toggle buttons. The 'Accumulate' popup lets you enter a text label\n" , 93 " to be drawn in the rendered image viewer -- the actual display of labels\n" , 94 " (size and location) is controlled from the image viewer intensity bar\n" , 95 " popup menu -- item (e) above. Right-Click lets you change the label\n" , 96 " for newly rendered images, whereas Shift+Right-Click lets you change\n" , 97 " the label for all previously rendered images as well as new images.\n" , 98 " (l) In the 'Clusters' report panel, right-clicking in the upper part of\n" , 99 " the window (where the textual summary is), will let you choose how\n" , 100 " the 'Histog' option will plot the histogram from the 'Aux.Dset'.\n" , 101 " ('Histog' is selected from the menu whose initial choice is 'Mean'.)\n" , 102 "--------------------------------------------------------------------------------\n" , 103 " ***** Hidden Clicks to Activate AFNI Features *****\n" , 104 "\n" , 105 "(3) Other 'special' clicks that aren't obvious:\n" , 106 " (a) Left-clicking on the 'Image' or 'Graph' button for an already open\n" , 107 " AFNI viewer will bring that viewer's window back up to the top of\n" , 108 " the X11 window stacking order.\n" , 109 " (b) Right-clicking on the 'Image' or 'Graph' button for an already open\n" , 110 " AFNI viewer will bring that viewer's window over to the place where\n" , 111 " you just clicked -- this is useful for finding lost viewers.\n" , 112 " (c) Right-clicking on the 'DataDir' button in the AFNI controller will\n" , 113 " un-hide (or re-hide) the obsolescent 'Define Markers' button.\n" , 114 " (d) Left-clicking on the logo at the lower left of a graph viewer will\n" , 115 " make the logo and menu buttons disappear -- this is intended to help\n" , 116 " you make a clean-looking snapshot of the window. Left-click again\n" , 117 " in the same region at the lower left to un-hide the logo and buttons.\n" , 118 " (e) Right-clicking on the graph viewer logo or on the image viewer 'Disp'\n" , 119 " button (i.e., the things at the lower left of each viewer window) will\n" , 120 " bring the parent AFNI controller back to the top of the X11 window\n" , 121 " stacking order.\n" , 122 " (f) In an image viewer window, if you press-and-hold-down the Left mouse\n" , 123 " button, then drag the cursor vertically and horizontally (while still\n" , 124 " holding the Left button down), the contrast and brightness of the\n" , 125 " grayscale underlay changes as you move the mouse.\n" , 126 " (g) To exit AFNI quickly when multiple controllers are open, hold down the\n" , 127 " Shift key when you press the 'done' button (in any AFNI controller).\n" , 128 " The usual requirement of pressing 'done' twice within 5 second is\n" , 129 " skipped, and all AFNI controllers exit immediately.\n" , 130 " (h) Left-clicking in the logo square to the right of the AFNI controller\n" , 131 " 'done' button will cause the AFNI splash screen to popup. You can\n" , 132 " close the splash screen window again via the usual X11 controls on\n" , 133 " the window border, or by left-clicking again in the logo square.\n" , 134 "--------------------------------------------------------------------------------\n" , 135 " ***** Keyboard Shortcuts: Image Viewer Window *****\n" , 136 "\n" , 137 "(4) The AFNI image viewer has many keyboard shortcuts. Help for these can be\n" , 138 " found by using 'BHelp' and then clicking on the image sub-window itself.\n" , 139 " The shortcuts are used by putting the mouse cursor over the image sub-window\n" , 140 " and pressing the keyboard key.\n" , 141 " a = fix window aspect ratio (= Left-click in intensity bar)\n" , 142 " c = enter cropping mode (= clicking the 'crop' button)\n" , 143 " D = open Disp control panel (= clicking the 'Disp' button)\n" , 144 " i = make the image sub-window smaller inside the overall viewer\n" , 145 " I = make the image sub-window larger\n" , 146 " l = left-right mirror image (= '+LR Mirror' on Disp panel)\n" , 147 " m = toggle 'Min-to-Max' on/off (= 'Min-to-Max' or '2%-to-98%' on Disp)\n" , 148 " M = open Montage control panel (= clicking the 'Mont' button)\n" , 149 " o = color Overlay on/off (= 'See Overlay' in AFNI controller)\n" , 150 " p = toggle panning mode (= clicking the 'pan' button)\n" , 151 " q = close window (= clicking the 'done' button)\n" , 152 " r = like 'v', but image 'rebounds' when it reaches end of count\n" , 153 " R = like 'r', but backwards order\n" , 154 " s = sharpen underlay image (= 'Sharpen' on the Disp control panel)\n" , 155 " S = save image (= clicking the 'Save' button)\n" , 156 " u = toggle background to be from Underlay or Overlay dataset\n" , 157 " v = automatically change images to make a 'video' (forwards order)\n" , 158 " V = same as 'v' but backwards order\n" , 159 " z = zoom out (= zoom down-arrow button)\n" , 160 " Z = zoom in (= zoom up-arrow button)\n" , 161 " [ = time index down by 1\n" , 162 " ] = time index up by 1\n" , 163 " { = lower AFNI statistical threshold slider\n" , 164 " } = raise AFNI statistical threshold slider\n" , 165 " > = PageUp = move forward one slice in image viewer\n" , 166 " < = PageDown = move backward one slice in image viewer\n" , 167 " # = toggle checkerboard pattern from underlay and overlay datasets\n" , 168 " 3 = turn checkerboard pattern off\n" , 169 " Keyboard arrow keys = move crosshairs (normal operation)\n" , 170 " = pan zoomed window (when 'pan' is on)\n" , 171 " Shift+arrow keys = pan cropped region around\n" , 172 " Ctrl+arrow keys = expand/shrink cropped region\n" , 173 " Home key = center zoomed window on current crosshair location\n" , 174 " Shift+Home = center cropped region on current crosshair location\n" , 175 " Del = undo in the Drawing plugin\n" , 176 " F2 = turn the Drawing pencil on\n" , 177 " F3 = subtract 1 from the Drawing plugin value\n" , 178 " F4 = add 1 to the Drawing plugin value\n" , 179 " F5 = Meltdown!\n" , 180 " F6 and higher are not (yet) defined.\n" , 181 "--------------------------------------------------------------------------------\n" , 182 " ***** Keyboard Shortcuts: Graph Viewer Window *****\n" , 183 "\n" , 184 "(5) The AFNI graph viewer also has many keyboard shortcuts.\n" , 185 " a = autoscale the graphs (this one time)\n" , 186 " A = autoscale the graphs (every time they are redrawn)\n" , 187 " b = switch graph baseline mode (between Separate, Common, and Global)\n" , 188 " B = switch on/off Boxes graphs instead of line graphs\n" , 189 " g = decrease vertical grid spacing in graphs\n" , 190 " G = increase vertical grid spacing in graphs\n" , 191 " h = draw dotted horizontal line at zero level in graphs\n" , 192 " i = decrease graph 'ignore' level by 1\n" , 193 " I = increase graph 'ignore' level by 1\n" , 194 " l = move to last time point\n" , 195 " L = turn AFNI logo on or off (but why would you want it OFF?!)\n" , 196 " m = reduce matrix size of sub-graphs by 1\n" , 197 " M = increase matrix size of sub-graphs by 1\n" , 198 " q = quit = Opt->Done\n" , 199 " r/R = 'rebound' up or down in time\n" , 200 " S = save an image of the graph window to a file\n" , 201 " t = show text (numbers) instead of graphs\n" , 202 " v/V = 'video' up or down in time\n" , 203 " w = write data from central sub-graph to a 1D file\n" , 204 " z = change slice number by 1 downwards (= keyboard Page Down key)\n" , 205 " Z = change slice number by 1 upwards (= keyboard Page Up key)\n" , 206 " - = scale the graphs down (vertically)\n" , 207 " + = scale the graphs up\n" , 208 " 1 = move to first time point\n" , 209 " < or [ = move back in time by 1 point (= keyboard Left arrow)\n" , 210 " > or ] = move up in time by 1 point (= keyboard Right arrow)\n" , 211 " N = after typing the 'N', type a number, then press Enter;\n" , 212 " the matrix of sub-graphs will change to the number given immediately\n" , 213 " F5 = Meltdown!\n" , 214 "--------------------------------------------------------------------------------\n" , 215 " ***** Keyboard Shortcuts in the Threshold Slider *****\n" , 216 "\n" , 217 "(6) Fine control over the threshold slider is hard with the mouse. You can\n" , 218 " move the slider with the following keystrokes, after clicking in the\n" , 219 " slider's 'thumb' to move the keyboard input focus to this control.\n" , 220 " Down arrow = reduce slider by 1 in the 4th significant place\n" , 221 " Up arrow = increase slider by 1 in the 4th significant place\n" , 222 " Page Down = reduce slider by 1 in the 3rd significant place\n" , 223 " Page Up = increase slider by 1 in the 3rd significant place\n" , 224 " Home = drop slider to 0\n" , 225 " End = move slider to top\n" , 226 " The Left and Right arrow keys can similarly be used in the image viewer\n" , 227 " slice index slider to move 1 slice backward or forward at a time.\n" , 228 "--------------------------------------------------------------------------------\n" , 229 NULL } ; 230 #define NUM_readme_afnigui 227 231