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3dANOVA.json
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3dANOVA.json
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{
"command-line": "3dANOVA [LEVELS] [DSET] [FTR] [MEAN] [DIFF] [CONTR] [BUCKET]",
"description": "tool description",
"inputs": [
{
"command-line-flag": "-levels",
"description": "r = number of factor levels",
"id": "LEVELS",
"name": "LEVELS",
"optional": true,
"type": "String",
"value-key": "[LEVELS]"
},
{
"command-line-flag": "-dset",
"description": "data set for factor level 1 . . .. . . -dset 1 filename data set for factor level 1 . . .. . . -dset r filename data set for factor level r . . .. . . -dset r filename data set for factor level r [-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 [-debug level] : request extra output 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 [-mean i prefix] : estimate of factor level i mean [-diff i j prefix] : difference between factor levels [-contr c1...cr prefix] : contrast in factor levels Modified ANOVA computation options: (December, 2005) ** 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). 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 N.B.: 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 'fred+orig[3]' Example of 3dANOVA: ------------------ Example is based on a study with one factor (independent variable) called 'Pictures', with 3 levels: (1) Faces, (2) Houses, and (3) Donuts The ANOVA is being conducted on the data of subjects Fred and Ethel: 3dANOVA -levels 3 \\ -dset 1 fred_Faces+tlrc \\ -dset 1 ethel_Faces+tlrc \\ \\ -dset 2 fred_Houses+tlrc \\ -dset 2 ethel_Houses+tlrc \\ \\ -dset 3 fred_Donuts+tlrc \\ -dset 3 ethel_Donuts+tlrc \\ \\",
"id": "DSET",
"name": "DSET",
"optional": true,
"type": "String",
"value-key": "[DSET]"
},
{
"command-line-flag": "-ftr",
"description": "-ftr Pictures \\",
"id": "FTR",
"name": "FTR",
"optional": true,
"type": "String",
"value-key": "[FTR]"
},
{
"command-line-flag": "-mean",
"description": "-mean 1 Faces \\",
"id": "MEAN",
"name": "MEAN",
"optional": true,
"type": "String",
"value-key": "[MEAN]"
},
{
"command-line-flag": "-diff",
"description": "-diff 1 2 FvsH \\",
"id": "DIFF",
"name": "DIFF",
"optional": true,
"type": "String",
"value-key": "[DIFF]"
},
{
"command-line-flag": "-contr",
"description": "-contr 1 1 -1 FHvsD \\",
"id": "CONTR",
"name": "CONTR",
"optional": true,
"type": "String",
"value-key": "[CONTR]"
},
{
"command-line-flag": "-bucket",
"description": "-bucket fred_n_ethel_ANOVA 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 = Sep 7 2018 {:}",
"id": "BUCKET",
"name": "BUCKET",
"optional": true,
"type": "String",
"value-key": "[BUCKET]"
}
],
"name": "tool name",
"schema-version": "0.5",
"suggested-resources": {
"cpu-cores": 1,
"ram": 1,
"walltime-estimate": 60
},
"tags": {},
"tool-version": "v0.1.0"
}