:orphan: .. _ahelp_p2dsetstat: ********** p2dsetstat ********** .. contents:: :local: | Overview ======== .. code-block:: none 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 ======= .. code-block:: none 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 ======= .. code-block:: none 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 ======== .. code-block:: none 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