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  

|
May 13, 2003 03:47PM

Hello Shayna:

I'm not sure if this is what you had in mind, but:

The residual is defined:
ei = Yi - Yhat
where
ei = ith residual
Yi = ith data point
Yhat = fitted value

The "standardized residual" is defined:
ri = ei / sqrt(MSE)
where
ri = ith standardized residual
MSE = estimate of the measurement variance

Program 3dDeconvolve can be used to calculate the single sample t-test of
population mean equal to zero, as follows:

First concatenate the datasets from each subject:
3dTcat -prefix myData Subj1+tlrc etc. etc. (do NOT use -rlt option)

Thus, dataset myData+tlrc contains one sub-brick for each subject.
Now use program 3dDeconvolve to calculate the t-test as follows:
3dDeconvolve -input myData+tlrc -mask myMask+tlrc -polort 0 \
-progress 10000 -tout -vout -bucket myTtest -errts myResid

The bucket dataset myTtest+tlrc contains 3 sub-bricks: sub-brick #0 contains
the sample mean across subjects at each voxel location; sub-brick #1 contains
the one-sample t-test values at each voxel location; and sub-brick #2 contains
the estimated error variance MSE. The dataset myResid+tlrc contains the
residual error at each voxel for each subject, where each sub-brick corresponds
to a different subject.

Now, to calculate the standardized residuals, use the 3dcalc commands:
3dcalc -a myResid+tlrc -b myTtest+tlrc'[2]' -expr "a/sqrt(b)" \
-fscale -prefix myStdRes

The output dataset myStdRes+tlrc will contain the standardized residuals
at each voxel location for each subject.

Please let me know how this works out.

Doug Ward
Subject Author Posted

single subject vs. group analysis

Shayna May 09, 2003 04:58PM

Re: single subject vs. group analysis

B. Douglas Ward May 13, 2003 03:47PM

Re: single subject vs. group analysis

Marina January 27, 2005 11:27AM