This program performs single factor Analysis of Variance (ANOVA)
on 3D datasets
---------------------------------------------------------------
Usage:
-----
3dANOVA
-levels r : r = number of factor levels
-dset 1 filename : 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 \
\
-ftr Pictures \
-mean 1 Faces \
-mean 2 Houses \
-mean 3 Donuts \
-diff 1 2 FvsH \
-diff 2 3 HvsD \
-diff 1 3 FvsD \
-contr 1 1 -1 FHvsD \
-contr -1 1 1 FvsHD \
-contr 1 -1 1 FDvsH \
-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 = Oct 31 2024 {AFNI_24.3.06:linux_ubuntu_24_64}
