AFNI program: 3dANOVA3
Output of -help
This program performs three-factor ANOVA on 3D data sets.
Usage:
3dANOVA3
-type k type of ANOVA model to be used:
k = 1 A,B,C fixed; AxBxC
k = 2 A,B,C random; AxBxC
k = 3 A fixed; B,C random; AxBxC
k = 4 A,B fixed; C random; AxBxC
k = 5 A,B fixed; C random; AxB,BxC,C(A)
-alevels a a = number of levels of factor A
-blevels b b = number of levels of factor B
-clevels c c = number of levels of factor C
-dset 1 1 1 filename data set for level 1 of factor A
and level 1 of factor B
and level 1 of factor C
. . . . . .
-dset i j k filename data set for level i of factor A
and level j of factor B
and level k of factor C
. . . . . .
-dset a b c filename data set for level a of factor A
and level b of factor B
and level c of factor C
[-voxel num] screen output for voxel # num
[-diskspace] print out disk space required for
program execution
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.)
[-fa prefix] F-statistic for factor A effect
[-fb prefix] F-statistic for factor B effect
[-fc prefix] F-statistic for factor C effect
[-fab prefix] F-statistic for A*B interaction
[-fac prefix] F-statistic for A*C interaction
[-fbc prefix] F-statistic for B*C interaction
[-fabc prefix] F-statistic for A*B*C interaction
[-amean i prefix] estimate of factor A level i mean
[-bmean i prefix] estimate of factor B level i mean
[-cmean i prefix] estimate of factor C level i mean
[-xmean i j k prefix] estimate mean of cell at factor A level i,
factor B level j, factor C level k
[-adiff i j prefix] difference between factor A levels i and j
(with factors B and C collapsed)
[-bdiff i j prefix] difference between factor B levels i and j
(with factors A and C collapsed)
[-cdiff i j prefix] difference between factor C levels i and j
(with factors A and B collapsed)
[-xdiff i j k l m n prefix] difference between cell mean at A=i,B=j,
C=k, and cell mean at A=l,B=m,C=n
[-acontr c1...ca prefix] contrast in factor A levels
(with factors B and C collapsed)
[-bcontr c1...cb prefix] contrast in factor B levels
(with factors A and C collapsed)
[-ccontr c1...cc prefix] contrast in factor C levels
(with factors A and B collapsed)
[-aBcontr c1 ... ca : j prefix] 2nd order contrast in A, at fixed
B level j (collapsed across C)
[-Abcontr i : c1 ... cb prefix] 2nd order contrast in B, at fixed
A level i (collapsed across C)
[-aBdiff i_1 i_2 : j prefix] difference between levels i_1 and i_2 of
factor A, with factor B fixed at level j
[-Abdiff i : j_1 j_2 prefix] difference between levels j_1 and j_2 of
factor B, with factor A fixed at level i
[-abmean i j prefix] mean effect at factor A level i and
factor B level j
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)
** These options apply to model types 4 and 5, only.
For details, see http://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).
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example: "classic" houses/faces/donuts for 4 subjects (2 genders)
(level sets are gender (M/W), image (H/F/D), and subject)
Note: factor C is really subject within gender (since it is
nested). There are 4 subjects in this example, and 2
subjects per gender. So clevels is 2.
3dANOVA3 -type 5 \
-alevels 2 \
-blevels 3 \
-clevels 2 \
-dset 1 1 1 man1_houses+tlrc \
-dset 1 2 1 man1_faces+tlrc \
-dset 1 3 1 man1_donuts+tlrc \
-dset 1 1 2 man2_houses+tlrc \
-dset 1 2 2 man2_faces+tlrc \
-dset 1 3 2 man2_donuts+tlrc \
-dset 2 1 1 woman1_houses+tlrc \
-dset 2 2 1 woman1_faces+tlrc \
-dset 2 3 1 woman1_donuts+tlrc \
-dset 2 1 2 woman2_houses+tlrc \
-dset 2 2 2 woman2_faces+tlrc \
-dset 2 3 2 woman2_donuts+tlrc \
-adiff 1 2 MvsW \
-bdiff 2 3 FvsD \
-bcontr -0.5 1 -0.5 FvsHD \
-aBcontr 1 -1 : 1 MHvsWH \
-aBdiff 1 2 : 1 same_as_MHvsWH \
-Abcontr 2 : 0 1 -1 WFvsWD \
-Abdiff 2 : 2 3 same_as_WFvsWD \
-Abcontr 2 : 1 7 -4.2 goofy_example \
-bucket donut_anova
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 4 5 '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'.
++ Compile date = Jul 24 2008
This page auto-generated on
Fri Jul 25 01:23:46 EDT 2008