--- afni Interactive steps (partial introduction to the afni GUI) --- Tasks: A. locate data, peruse main afni GUI 1. go to AFNI_data6/afni and verify there are datasets --> cd ~/AFNI_data6/afni ; ls ; afni & 2. quickly peruse the main window - coords, Ulay Image/Graph buttons, BHelp, -> panel toggle buttons B. examine anat+orig as underlay 1. set anat+orig as Underlay, open windows, open/close graph 2. note xhairs, cardinal views, contrast/brightness controls (mouse/buttons) 3. compare against Min-to-Max display (in Disp window) 4. zoom, pan, crop 5. other menus: right-click in image and in color bar C. review alignment between anat+orig and epi_r1_orig 1. set epi_r1+orig as Overlay 2. look at edges, CSF (jump-to-xyz: 20 8 57) 3. turn off/on overlay (toggle button and get 'o' from F1 help) 4. threshold overlay D. review time series, look for motion or other problems 1. set epi_r1+orig as Underlay, turn off overlay 2. note graph information, graph size and relation to Image window - note Opt->Scale/Matrix and keyboard shortcuts 3. jump-to-ijk: 22 27 16 (via right-click in image) 4. ignore 3 TRs (FIM -> Ignore) 5. evaluate motion : 'v'ideo mode (space to stop), arrows 6. pick ideal: (FIM -> Pick Ideal -> epi_r1_ideal.1D) 7. jump-to-ijk: 20 67 16 (via right-click in image) E. overlay statistics: evaluate full-F and maybe fpos stimulus 1. set func_slim+orig as overlay, Full_Fstat as both OLay, Thr 2. set threshold to 7.0, evaluate colored/uncolored voxels - note Thr range and individual voxel values 3. evaluate colors of voxels, Inten range, OLay range, scalar, Pos button - note color at individual voxels - alter one panel range and color 4. set thresh -> 12.0, simple Clusterize, look at report (Rpt) 5. (optional) 4x3x2 coronal montage around peak F, save .jpg image 6. change OLay, Thr sub-bricks to 1,2 (Vrel Coef and Tstat) - set p=0.001, note q - set color range to 2, 7 Positive colors - change one color panel range and color 7. (optional) 3 hidden menus (note cursor color), consider other color bars ------------- optional, continued ------------------------------------ F. (optional) histogram plugin: 1. strip+orig, note background, CSF, gray and white peaks - plot, range 100-4000, 100 bins G. (optional) dataset information: how was func_slim created? 1. Define Databmode -> Misc -> OLay info 2. note orientation, extents, HISTORY and sub-brick contents H. (optional) standard space: 1. where is the peak F-stat? - Underlay -> anat, and switch to "Talairach View" - Image window -> right click -> Where Am I? 2. Atlas Colors: hippocampus -> blue, amygdala -> red