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