:orphan: .. _ahelp_3dANOVA2: ******** 3dANOVA2 ******** .. contents:: :local: | This program performs a two-factor Analysis of Variance (ANOVA) on 3D datasets. Please also see (and consider using) AFNI's gen_group_command.py program to construct your 3dANOVA2 command. That program helps simplify the process of specifying your command. Usage ===== .. code-block:: none 3dANOVA2 -type k : type of ANOVA model to be used: k=1 fixed effects model (A and B fixed) k=2 random effects model (A and B random) k=3 mixed effects model (A fixed, B random) -alevels a : a = number of levels of factor A -blevels b : b = number of levels of factor B -dset 1 1 filename : data set for level 1 of factor A and level 1 of factor B . . . . . . -dset i j filename : data set for level i of factor A and level j of factor B . . . . . . -dset a b filename : data set for level a of factor A and level b of factor B [-voxel num] : screen output for voxel # num [-diskspace] : print out disk space required for program execution [-mask mset] : use sub-brick #0 of dataset 'mset' to define which voxels to process The following commands generate individual AFNI 2-sub-brick datasets: (In each case, output is written to the file with the specified prefix file name.) [-ftr prefix] : F-statistic for treatment effect [-fa prefix] : F-statistic for factor A effect [-fb prefix] : F-statistic for factor B effect [-fab prefix] : F-statistic for interaction [-amean i prefix] : estimate mean of factor A level i [-bmean j prefix] : estimate mean of factor B level j [-xmean i j prefix] : estimate mean of cell at level i of factor A, level j of factor B [-adiff i j prefix] : difference between levels i and j of factor A [-bdiff i j prefix] : difference between levels i and j of factor B [-xdiff i j k l prefix] : difference between cell mean at A=i,B=j and cell mean at A=k,B=l [-acontr c1 ... ca prefix] : contrast in factor A levels [-bcontr c1 ... cb prefix] : contrast in factor B levels [-xcontr c11 ... c1b c21 ... c2b ... ca1 ... cab prefix] : contrast in cell means The following command generates one AFNI 'bucket' type dataset: [-bucket prefix] : create one AFNI 'bucket' dataset whose sub-bricks are obtained by concatenating the above output files; the output 'bucket' is written to file with prefix file name Modified ANOVA computation options: (December, 2005) ======================================================= .. code-block:: none ** These options apply to model type 3, only. For details, see https://afni.nimh.nih.gov/sscc/gangc/ANOVA_Mod.html [-old_method] : request to perform ANOVA using the previous functionality (requires -OK, also) [-OK] : confirm you understand that contrasts that do not sum to zero have inflated t-stats, and contrasts that do sum to zero assume sphericity (to be used with -old_method) [-assume_sph] : assume sphericity (zero-sum contrasts, only) This allows use of the old_method for computing contrasts which sum to zero (this includes diffs, for instance). Any contrast that does not sum to zero is invalid, and cannot be used with this option (such as ameans). Examples of 3dANOVA2 ==================== .. code-block:: none (And see also AFNI's gen_group_command.py for what might is likely a simpler method for constructing these commands.) 1) This example is based on a study with a 3 x 4 mixed factorial: design: Factor 1 - DONUTS has 3 levels: (1) chocolate, (2) glazed, (3) sugar Factor 2 - SUBJECTS, of which there are 4 in this analysis: (1) fred, (2) ethel, (3) lucy, (4) ricky 3dANOVA2 \ -type 3 -alevels 3 -blevels 4 \ -dset 1 1 fred_choc+tlrc \ -dset 2 1 fred_glaz+tlrc \ -dset 3 1 fred_sugr+tlrc \ -dset 1 2 ethel_choc+tlrc \ -dset 2 2 ethel_glaz+tlrc \ -dset 3 2 ethel_sugr+tlrc \ -dset 1 3 lucy_choc+tlrc \ -dset 2 3 lucy_glaz+tlrc \ -dset 3 3 lucy_sugr+tlrc \ -dset 1 3 ricky_choc+tlrc \ -dset 2 3 ricky_glaz+tlrc \ -dset 3 3 ricky_sugr+tlrc \ -amean 1 Chocolate \ -amean 2 Glazed \ -amean 3 Sugar \ -adiff 1 2 CvsG \ -adiff 2 3 GvsS \ -adiff 1 3 CvsS \ -acontr 1 1 -2 CGvsS \ -acontr -2 1 1 CvsGS \ -acontr 1 -2 1 CSvsG \ -fa Donuts \ -bucket ANOVA_results The -bucket option will place all of the 3dANOVA2 results (i.e., main effect of DONUTS, means for each of the 3 levels of DONUTS, and contrasts between the 3 levels of DONUTS) into one big dataset with multiple sub-bricks called ANOVA_results+tlrc. Notes ===== .. code-block:: none For this program, the user must specify 1 and only 1 sub-brick with each -dset command. That is, if an input dataset contains more than 1 sub-brick, a sub-brick selector must be used, e.g.: -dset 2 4 'fred+orig[3]' INPUT DATASET NAMES This program accepts datasets that are modified on input according to the following schemes: 'r1+orig[3..5]' {sub-brick selector} 'r1+orig<100..200>' {sub-range selector} 'r1+orig[3..5]<100..200>' {both selectors} '3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation} For the gruesome details, see the output of 'afni -help'. Also see HowTo #5: Group Analysis on the AFNI website: https://afni.nimh.nih.gov/pub/dist/HOWTO/howto/ht05_group/html/index.shtml STORAGE FORMAT: The default output format is to store the results as scaled short (16-bit) integers. This truncantion might cause significant errors. If you receive warnings that look like this: *+ WARNING: TvsF[0] scale to shorts misfit = 8.09% -- *** Beware then you can force the results to be saved in float format by defining the environment variable AFNI_FLOATIZE to be YES before running the program. For convenience, you can do this on the command line, as in 3dANOVA -DAFNI_FLOATIZE=YES ... other options ... Also see the following links: https://afni.nimh.nih.gov/pub/dist/doc/program_help/common_options.html https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.environment.html ++ Compile date = Apr 18 2024 {AFNI_24.1.03:linux_ubuntu_16_64}