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  

|
September 03, 2015 02:07AM
Tent to PSC
Background (2 conditions 22 TR locked estimates/additional 22 RT auxiliary parameter estimates for each condition)

A.
I have a few questions in regards to the issue of PSC with Tent functions. To put it simply I want to get ((target-baseline)/baseline)*100) for each of my time points covered by my tent function. I have 3 trend terms (linear, quadratic, cubic) and I was wondering how to include them in my baseline along with the intercept (maybe AFNI is already doing this in the scaling). I tried employing scaling prior to 3dconvolve, will this will obviously not include my baseline terms since regression has not been conducted yet. How could I go about incorporating them? (tcsh material posted below)

B.
[afni.nimh.nih.gov]
The link posted above has me under the impression that if properly used SCALE then the beta coefficients for my predictors of interest are interpretable as percent signal changes. If I am mistaken what is the best method for converting my beta coefficients to PSC?
Obtained with afni_proc.py (seems to have mean set to 100)
# ================================= scale ==================================
# scale each voxel time series to have a mean of 100
# (be sure no negatives creep in)
# (subject to a range of [0,200])
foreach run ( $runs )
3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc
3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc \
-c mask_epi_extents+tlrc \
-expr 'c * min(200, a/b*100)*step(a)*step(b)' \
-prefix pb04.$subj.r$run.scale
end

C.
I have been extracting my coeffs from the sub-bricks in my stats file. What does iresp file give me(maybe I should use it instead)?

D.
How can I find out if my stats file includes standard errors for my beta coefficients?

Thanks for your help
Subject Author Posted

Tent to PSC Question

s1110a September 03, 2015 02:07AM

Re: Tent to PSC Question

rick reynolds September 03, 2015 09:39AM

Re: Tent to PSC Question

s1110a September 03, 2015 02:24PM

Re: Tent to PSC Question

rick reynolds September 03, 2015 03:53PM

Re: Tent to PSC Question

s1110a September 03, 2015 08:05PM