Hi AFNI-sages. It was a while ago I ran amplitude modulation analysis in AFNI. I have a few questions to make sure I'm doing it right. Thanks in advance!

First assumation: This is the exampel to look at in the afni proc documentation:

Quote
afni_proc
NARPS. Applied NARPS example from AFNI. ~2~

(recommended? yes, reasonable for a complete analysis)

An amplitude modulation task analysis.

1) First thing I notice is that this pre-proc, in contrast to the non-AM task analysis, has anaticor (and thus freesurfer parcels) as recommended settings:

-anat_follower_ROI FS_wm_e epi SUMA/mask.aseg.wm.e1.nii.gz \
                 -anat_follower_ROI FS_REN_epi epi                          \
                     SUMA/aparc+aseg_REN_all.nii.gz                         \
                 -anat_follower_ROI FS_REN_anat anat                        \
                     SUMA/aparc+aseg_REN_all.nii.gz                         \
                 -anat_follower_erode FS_wm_e                               \
               -regress_anaticor_fast                                     \
                 -regress_anaticor_fwhm 20 
                  -regress_anaticor_label FS_wm_e                            \
                  -regress_make_corr_vols FS_wm_e                            \

Why is this? Is anaticor extra important for AM analysis?

2) In the example there are two regressors, "Resp" and "NoResp". I assume Resp has an amplitude modulator and NoResp does not.
That is why Resp has the AM2 stim type and NoResp has the AM1 stim type.

-regress_stim_times timing/times.Resp.txt                  \
                     timing/times.NoResp.txt                                \
                 -regress_stim_labels Resp NoResp                           \
                 -regress_stim_types AM2 AM1                                \
                 -regress_basis_multi dmBLOCK                               \

With the regress basis "dmBlock" I assume the stim files should look something like this?

Resp: (dmBlock + AM2)
10.704311*-1.088090:0.0001 14.650165*-0.189424:0.0001 18.894507*0.520777:0.0001
(first onset at 10.7 seconds, with modulator -1.088.. with duration 0.0001

NoResp:  (dmBlock + AM1)
6.592667:0.0001 
(first onset 6.59 with duration 0.0001, no modulation)

And if e.g. NoResp would be empty for a subject, then we can do something like:

-10:0.0001

3) The contrast (gltsym) has this syntax:

                 -regress_opts_3dD -jobs 8 -gltsym 'SYM: Resp[1] -Resp[2]'  \
                     -glt_label 1 gain-loss -GOFORIT 10

What is the meaning of Resp[1] -Resp[2]?
Does this mean Resp-no-modulation MINUS resp-with-modulation? The name of it is gain-loss.

We have only one AM2 regressor (feedback) which is modulated with a value related to their decsion making (the other regressor are missed responsen, that is why we use AM1 and no modulator). When running the pre-proc we end up with 2 feedbacks in the stats-file, I assumed the feedback#0_coef is the unmodulated feedback regressor coef and feedback#1_coef is the modulated feedback regressor coef.
Does -gltsym 'SYM: Resp[1] -Resp[2]' mean the contrast of those two? And what is the meaning of that versus just using feedback#1_coef in the subsequent ttests?

My code looks like this:

-regress_stim_types AM2 AM1 \
    -regress_stim_labels feedback miss \
    -regress_basis 'dmBLOCK' \

Should I add

-regress_opts_3dD -jobs 8 -gltsym 'SYM: feedback [1] -feedback [2]'  \
                     -glt_label 1 feed-feedAM

4 and final)
This is an event design. The stimuli is shorter than 1s.
Can I do what I did above and just use a super short dmBlock duration? Example from my AM2 regressor:
10.704311*-1.088090:0.0001
Using 0.0001s duration.

BIG THANKS!



Edited 1 time(s). Last edit at 01/28/2022 09:43AM by Robin.