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.
