p2dsetstat¶
Overview¶
This program converts a p-value to a statistic of choice, with
reference to a particular dataset.
Often to convert a p-value to a statistic, supplementary
information is needed, such as number of degrees of freedom. AFNI
programs that write statistics *do* store that info in headers, and
this program is meant to be a useful to do conversions based on
that info. Here, the user provides the p-value and the specific [i]th
brick of the dataset in question, and a statistic (either as single number,
or with supplementary info) is output to screen.
This program should give equivalent results to other AFNI programs
like ccalc and cdf, but with less work by the user.
See also the complementary program for doing the inverse, converting
a statistic to an equivalent p-value: dsetstat2p.
**Note that the user will have to choose explicitly whether they
are doing one-sided or bi-sided/two-sided testing!** This is
equivalent to choosing "Pos&Neg" or just "Pos" (or just "Neg",
if the user multiplies the output by a negative) in the AFNI
GUI's clickable p-to-statistic calculator.
written by : PA Taylor and RC Reynolds (SSCC, NIMH, NIH)
version : 2.0
rev date : Nov 04, 2023
Options¶
p2dsetstat \
-inset DDD"[i]" \
-pval P \
-bisided|-2sided|-1sided \
{-quiet}
where:
-inset DDD"[i]"
:specify a dataset DDD and, if it has multiple sub-bricks,
the [i]th subbrick with the statistic of interest MUST
be selected explicitly; note the use of quotation marks
around the brick selector (because of the square-brackets).
Note that 'i' can be either a number of a string label
selector.
NB: we refer to "sub-bricks" here, but the inset
could also be a surface dataset, too.
-pval P :input p-value P, which MUST be in the interval (0,1).
-bisided
or
-2sided
or
-1sided :one of these sidedness options MUST be chosen, and it is
up to the researcher to choose which is appropriate.
-quiet :an optional flag so that output ONLY the final statistic
value is output to standard output; this can be then be
viewed, redirected to a text file or saved as a shell
variable. (Default: display supplementary text.)
Outputs¶
The types of statistic values that can be calculated are:
corr coef, t-stat, F-stat or z-score.
If "-quiet" is used, then basically just a single number (the converted
statistic value) is output. See examples for saving this in a file or
variable.
Without the "-quiet" option, some descriptive text is also output with
the calculation, stating what kind of statistic is being output, etc.
Sidenote: another way to get stat+parameter information is via 3dAttribute,
and in particular asking for the "BRICK_STATAUX" information. That output
is probably a bit more cryptic, but it is described on the attributes page,
which users may look upon here:
https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.attributes.html
and tremble.
Examples¶
In all cases note the use of the single quotes around the subbrick
selector-- these are necessary in some shell types!
1) Do a calculation and display various information to screen:
p2dsetstat \
-inset stats.sub01+tlrc"[2]" \
-pval 0.001 \
-bisided
2) Do a calculation and just display a single number (and also
use a string label to conveniently select the subbrick):
p2dsetstat \
-inset stats.sub01+tlrc"[Full_Fstat]" \
-pval 0.0005 \
-1sided \
-quiet
3) Do a calculation and store the output number as a variable,
here using tcsh syntax:
set my_stat = `p2dsetstat \
-inset stats.sub02+tlrc"[8]" \
-pval 0.001 \
-bisided \
-quiet`
4) Do a calculation and store the output number into a text
file:
p2dsetstat \
-inset stats.sub02+tlrc"[8]" \
-pval 0.001 \
-bisided \
-quiet > MY_STAT_FILE.txt
