AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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April 01, 2015 11:55AM
If you type the command
3dinfo -verb stats.Imagination001_REML+orig
you will get a screen printout of the information in the dataset header. The information for each volume (=sub-brick) in the dataset will include the type of statistic it is (t or F), and the degrees of freedom.

With that information, you can convert the voxel values from statistics to nominal p-values via 3dcalc. For example, if you find that volume #4 is a t-statistic with 27 degrees of freedom, you can convert it to a p-value with a command like
3dcalc -a stats.Imagination001_REML+orig'[4]' -expr 'fitt_t2p(a,27)' -datum float -prefix brick4p
There is no command to convert all the volumes directly to p-values -- just one at a time, as in the example above. Since you seem to be new to AFNI, I'll mention that volume counting in AFNI starts at 0 -- the first volume in a dataset is #0, the second volume is #1, and so on.

You might want to consider using the expression '-log10(fitt_t2p(a,27))' to save the negative of logarithm (base 10) of each p-value. That way, smaller p-values become large output values, and so they behave as you might expect when thresholding in the AFNI interface.
Subject Author Posted

is it possible to obtain p-values on output of 3dREMLfit

maitra April 01, 2015 01:13AM

Re: is it possible to obtain p-values on output of 3dREMLfit

gang April 01, 2015 09:55AM

Re: is it possible to obtain p-values on output of 3dREMLfit

maitra April 01, 2015 11:34AM

Re: is it possible to obtain p-values on output of 3dREMLfit

Emperor Zhark April 01, 2015 11:55AM

Re: is it possible to obtain p-values on output of 3dREMLfit

maitra April 01, 2015 03:47PM

Re: is it possible to obtain **one-sided** p-values on output of 3dREMLfit

maitra April 02, 2015 11:18PM

Re: is it possible to obtain **one-sided** p-values on output of 3dREMLfit

gang April 03, 2015 09:53AM

Re: is it possible to obtain **one-sided** p-values on output of 3dREMLfit

maitra April 03, 2015 10:04AM

Re: is it possible to obtain **one-sided** p-values on output of 3dREMLfit

gang April 03, 2015 10:21AM

Re: is it possible to obtain **one-sided** p-values on output of 3dREMLfit

maitra April 03, 2015 10:29AM