I have a large sample of task-based fMRI’s in an event-related design. There was only a single run for each participant. Participants either respond or not respond to a target or foil image. So there are four events I want to model in the GLM for each subject:
1: RT: Response to target
2. RF: Response to foil
3. NT: No response to target
4. NF: No response to foil
For each subject, there is a respective stimulus file containing timings associated with the four event types. Suppose they are respectively called RT.1D, RF.1D, NT.1D, and NF.1D. Lines in the afni_proc.py command would look like:
-regress_stim_times RT.1D RF.1D NT.1D NF.1D \ -regress_stim_labels RT RF NT NF \ -regress_local_times \ .... - -num_glt 6 \ -gltsym 'SYM: +RT' -glt_label 1 'beta_RT' \ -gltsym 'SYM: +RF' -glt_label 2 'beta_RF' \ -gltsym 'SYM: +NT' -glt_label 3 'beta_NT' \ -gltsym 'SYM: +NF' -glt_label 4 'beta_NF' \ -gltsym 'SYM: +RT -RF' -glt_label 5 'beta_RT_minus_RF' \ -gltsym 'SYM: +NT -NF' -glt_label 6 'beta_NF_minus_NF' \ ...
Since I’m runing many subjects, I want to use the same afni_proc.py script with environmental variable for subject ID used to specify directories and raw files.
There may be some subjects who, for example, never responded to a foil (i.e., #RF = 0). or responsed to all targets (#NT = 0). In this case, the RF.1D file or NT.1D files would be empty. Outside of using further bash scripting + environmental variables for referring to file names, can AFNI recognize an empty file as referring to no stimulus taking place? So if #RF = 0, the above code would produce a GLM with only three covariates for RT, NT, and NF? Similarly, the GLT’s containing references to RF (under labels 2 & 5) would not be evaluated.
I read the 3dDeconvolve documention, which states
*** In the case where the stimulus doesn't actually exist in the
data model (e.g., every line in 'tname' is a '*'), you will also have to use the '-allzero_OK' option to force 3dDeconvolve to run with regressor matrix columns that are filled with zeros.
Does this mean I can use the same script for every subject, even if one of the classes — NT, NF, RT, or RF — has no stimulus, so long as I include the option “-allzero_OK”?
Thank you for your attention.