AFNI program: fdrval
Output of -help
Usage: fdrval [options] dset sub val [val ...]
Reads FDR curve data from the header of dset for sub-brick
#sub and computes the q-value when the sub-brick statistical
threshold is set to val.
OPTIONS
-------
-pval = also output the p-value (on the same line, after q)
-ponly = don't output q-values, just p-values
-qonly = don't output p-values, just q-values [the default]
-qinput = The 'val' inputs are taken to be q-values and then the
*OR* outputs are the corresponding statistical thresholds.
-inverse This is the inverse of the usual operation.
* With this option, all 'val' inputs must be between 0 and 1
(exclusive), or bad things will happen and the program will
send e-mail to your mother explaining how stupid you are.
* You cannot use '-ponly' or '-pval' with this option.
* For example, if you do
fdrval dset+orig 1 1.2
and get a q-value of 0.234, then
fdrval -qinput dset+orig 1 0.234
should return the value 1.2 -- the original threshold.
(There may be a small discrepancy, due to the differences)
(between forward interpolation and inverse interpolation.)
* To set a (csh) variable to use in a script for thresholding
via 3dcalc, you could do something like
set tval = `fdrval -qinput dset+orig 1 0.05`
3dcalc -expr "step(a-$tval)" -a dset+orig'[1]' -prefix dmask
NOTES
-----
* Output for each 'val' is written to stdout.
* If the q-value can't be computed, then 1.0 will be output.
* If you input an absurdly high threshold, you will get the smallest
q-value stored in the dataset header. (This is not necessarily exactly
the smallest q-value that was computed originally, due to the way the
FDR curves are calculated and interpolated.)
* If you use '-qinput' and input a q-value that is too small for the
FDR curve in the dataset header, you will get a threshold at or above
the largest value in that sub-brick.
* Sample usage:
fdrval Fred_REML+orig 0 `count_afni -scale 0.1 10 20` | 1dplot -stdin
Uses the 'count' program to input a sequence of values, and then
pipes into the 1dplot program to make a graph of F vs. q.
* See the link below for information on how AFNI computes FDR curves:
https://afni.nimh.nih.gov/pub/dist/doc/misc/FDR/FDR_Jan2008.pdf
* Also see the output of '3dFDR -help'
-- A quick hack by RWCox -- 15 Oct 2008 -- PG Wodehouse's birthday!
-- Quick re-hack to add '-qinput' option -- 20 Dec 2011 -- RWCox
-- Re-re-hack to make super-small '-qinput' values work right -- 14 Mar 2014
++ Compile date = Dec 17 2024 {AFNI_24.3.10:linux_ubuntu_24_64}
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Tue Dec 17 06:55:12 PM EST 2024