Gosset (Student) t-test sets of 3D datasets
for comparing the mean of 1 set of datasets against a constant.
** or use -base1_dset
- Also see the newer program 3dttest++, which lets you *
** include covariates to be regressed out of the data. **
* For most purposes, 3dttest++ is to be preferred over *
OUTPUTS:
A single dataset is created that is the voxel-by**-voxel** difference of the mean of set2 minus the mean of set1 (or minus ‘bval’). The output dataset will be of the intensity+Ttest (‘fitt’) type. The t-statistic at each voxel can be used as an interactive thresholding tool in AFNI.
the first set. The mean of set1 will be tested with a 2-sample t-test against the mean of set2.
N.B.: -set1 and -base1 are mutually exclusive!
- -base1_dset DSET = Similar to -base1, but input a dataset where bval
- can vary over voxels.
- -sdn1 sd n1 = If this option is given along with ‘-base1’, then
- ‘bval’ is taken to have standard deviation ‘sd’ computed from ‘n1’ samples. In this case, each voxel in set2 is compared to bval using a pooled-variance unpaired 2-sample t-test. [This is for Tom Johnstone; hope we meet someday.]
- -set2 datasets ... = Specifies the collection of datasets to put into
- the second set. There must be at least 2 datasets in each of set1 (if used) and set2.
- -paired = Specifies the use of a paired-sample t-test to
compare set1 and set2. If this option is used, set1 and set2 must have the same cardinality.
- N.B.: A paired test is intended for use when the set1 and set2
- dataset function values may be pairwise correlated. If they are in fact uncorrelated, this test has less statistical ‘power’ than the unpaired (default) t-test. This loss of power is the price that is paid for insurance against pairwise correlations.
- -unpooled = Specifies that the variance estimates for set1 and
set2 be computed separately (not pooled together). This only makes sense if -paired is NOT given.
- N.B.: If this option is used, the number of degrees
- of freedom per voxel is a variable, rather than a constant.
- -dof_prefix ddd = If ‘-unpooled’ is also used, then a dataset with
prefix ‘ddd’ will be created that contains the degrees of freedom (DOF) in each voxel. You can convert the t-value in the -prefix dataset to a z-score using the -dof_prefix dataset using commands like so:3dcalc -a ‘pname+orig[1]’ -b ddd+orig
-datum float -prefix ddd_zz -expr ‘fitt_t2z(a,b)’
- 3drefit -substatpar 0 fizt ddd_zz+orig
- At present, AFNI is incapable of directly dealing with datasets whose DOF parameter varies between voxels. Converting to a z-score (with no parameters) is one way of getting around this difficulty.
- -voxel voxel = like 3dANOVA, get screen output for a given voxel.
- This is 1-based, as with 3dANOVA.
The -base1 or -set1 command line switches must follow all other options (including those described below) except for the -set2 switch.
INPUT EDITING OPTIONS: The same as are available in 3dmerge.
OUTPUT OPTIONS: these options control the output files.
-session dirname = Write output into given directory (default=./) -prefix pname = Use ‘pname’ for the output directory prefix
(default=tdif)
-datum type = Use ‘type’ to store the output difference in the means; ‘type’ may be short or float. How the default is determined is described in the notes below.
** This program cannot deal with time-dependent or complex-valued datasets! ** By default, the output dataset function values will be shorts if the
first input dataset is byte- or short-valued; otherwise they will be floats. This behavior may be overridden using the -datum option.
(the single quotes are necessary). If you want to use ALL the sub-bricks from a multi-volume dataset, you can’t just give the dataset filename – you have to use
datasetname+orig’[0-$]’ or datasetname’[0..$]’
Otherwise, the program will reject the dataset as being too complicated for its pitiful understanding. [New in July 2007]
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 = Dec 16 2015