Hi, I am analyzing a fairly straight forward block design experiment, but in addition to estimating the stimulus driven activity I need to estimate the activity from individual blocks of fixation. Here it would seemingly make more sense to avoid adding any HRF to the model during these blocks (but of course keep the HRF for the stimulus blocks) but is there a way to do this with 3dDeconvolve? Using the stim_times_IM option I see that it is possible to obtain the beta weights for each block of the experiment, but what is the appropriate way to obtain an estimate of activity during individual blocks of rest?
[b]If for example, I wanted to do a linear contrast of the second fixation block vs. the 4th fixation block (there are actual reasons for wanting to do this), is there a way to do this without indicating a basis function for these periods of fixation? I feel that:
3dDeconvolve input expdata+tlrc.HEAD
stim_times_IM 1 Fixate.1D ‘BLOCK(20,1)’
stim_times_IM 2 Stimulus.1D ‘BLOCK(20,1)’
is problematic since it would be modeling the resting blocks explicitly.[/b]
Is it preferable to avoid this completely and instead extract the residuals of these time points from the nuisance regressors, via 3dTproject, separately?
Any advice would be greatly appreciated, thank you so much for your time.
db
What you want to do does not fix exactly into the AFNI analysis model, where we have a global “baseline” model (which includes the mean and slow drifts up/down), and we don’t have a local “baseline” model.
Below is my quick jetlagged outline of how you could do such an analysis in AFNI. However, there are probably not enough details here unless you are already a pretty expert AFNI user. If you want to proceed, you should first try to understand this, and then get back to me. Note that I am traveling to Italy for OHBM and so responses will probably be slow.
The way to analyze this model is to replace the mean component of our baseline model, and then provide stim_times for the control (fixation) task. The times and BLOCK durations should be such that the entire imaging run is covered, in the sense that the sum of all the regressors of interest is constant = 1.
Here’s a toy example:
 file A.1D = 10 30 50 70 90
 file B.1D = 20 40 60 80 100
Commands:
 3dDeconvolve nodata 150 1 num_stimts 2 stim_times 1 A.1D ‘BLOCK(10,1)’ stim_times 2 B.1D ‘BLOCK(10,1)’ polort 1 x1D Xmat.1D
 1deval a Xmat.1D’[0]’ b Xmat.1D’[1]’ expr a+b  1dplot stdin
I attached an image from the last command, which (if present) shows that in the middle of this 150s time period, where the stim_times are present, the sum of the 2 interleaved stimuli is close to being constant = 1.
So if this was your data and model, you could analyze the data by

removing the mean (constant = 1) regression component from the X matrix

only analyzing the time points where the sum of the stimulus response models is about 1 (20s to 110s in this example)

you could use stim_times_IM to get individual betas for each interval
One difficulty is that 3dDeconvolve does not provide any way to remove the mean regressor from the model without removing the higher order polynomials (which have zero mean over time) that represent slow drifts. For real data, it is important to include these drift components. Without modifying 3dDeconvolve, you could still do this analysis with the drift components by using option ‘polort 1’ to remove ALL polynomial components, then providing those polynomial slow regressors directly yourself using the ‘ortvec’ option. To construct those polynomial regressors for a single imaging run, you would do something like this:

3dDeconvolve input DATASET_NAME polort 4 x1D Xmat.1D x1D_stop num_stimts 1 stim_times 1 ‘1D: *’ ‘BLOCK(1)’
File Xmat.1D will have 6 columns:
#0 = all ones = constant regressor (give mean for baseline model)
#14 = polynomial of order 14 for the slow drift baseline model
#6 = all zeros = the fake stimulus with no actual information (since 3dDeconvolve requires 1 stimulus input)
You can extract columns #14 into a separate file with a command like
 1dcat Xmat.1D’[1…4]’ > Xpolort.1D
And then plot them (to be sure they are good) with
 1dplot Xpolort.1D
And then provide these to 3dDeconvolve with
 3dDeconvolve input DATASET_NAME polort 1 ortvec Xpolort.1D num_stimts XXXXXXX
An important detail is what I mentioned above  that you only analyze the data where the sum of the stimulus regressors is essentially constant. You should examine the X matrix to make sure this sum of stimulus regressors is correct.