Hello afni experts,
I have a question regarding setting up my 3dDeconvolve model after I have done all the initial preprocessing steps for a generalized PPI analysis.
I conducted a typical differential delay fear conditioning task with a fear acquisition phase and a fear extinction phase. In my initial 3dDeconvolve model prior to conducting a PPI, I had both the fear acquisition run and my fear extinction run within the same model. So, within my timing files, for my acquisition stimuli, I had my times for the first run and an "*" to serve as a place holder for the second run (fear extinction). Similarly for my fear extinction stimuli, I had an "*" for the first run (fear acquisition) and my timing for the fear extinction stimuli for my second run.
So for my PPI analysis, I have a CS+ Interaction term during aquisition, a CS- Interaction term for aquisition, a CS+ Interaction term for extinction, and a CS- interaction term for extinction.
My question is, since I had incorporated both fear aquisition and fear extinction in my initial model, is it possible to incorporate all acquisition and extinction interaction terms for my 3dDeconvolve for the PPI? Would I need a row of zeros within each of the these interaction terms as place holders for when fear extinction or when fear aquisition is off? I guess how would I let the program know that the scaled run1 goes with fear aquisition and the scaled run 2 goes with fear extinction?
Additionally I need to put the seed in as a regressor (so I have the seed times series during acqusition and then the time series during extinction). Again I am not sure how to let the program know that one regressor goes with one run and the other goes with run two.
I am sorry if I am making this confusing . Below is my initial 3dDeconvolve model:
# run the regression analysis
3dDeconvolve -input ${subfolder}/${subject}/${subject}.${results}/pb04.${subject}.r*.scale.nii \
-censor ${subfolder}/${subject}/${subject}.${results}/censor_${subject}_combined_2_FNIRT_3.5.1D \
-polort 2 \
-num_stimts 10 \
-stim_times 1 ${subfolder}/${subject}/${subject}.${results}/stimuli/Order2_CSa_ACQ.1D 'TENT(0,14,8)' \
-stim_label 1 CSaACQ \
-stim_times 2 ${subfolder}/${subject}/${subject}.${results}/stimuli/Order2_CSb_ACQ.1D 'TENT(0,14,8)' \
-stim_label 2 CSbACQ \
-stim_times 3 ${subfolder}/${subject}/${subject}.${results}/stimuli/Order2_CSa_EXT.1D 'TENT(0,14,8)' \
-stim_label 3 CSaEXT \
-stim_times 4 ${subfolder}/${subject}/${subject}.${results}/stimuli/Order2_CSb_EXT.1D 'TENT(0,14,8)' \
-stim_label 4 CSbEXT \
-stim_file 5 ${subfolder}/${subject}/${subject}.${results}/motion_demean_FNIRT_3.5.1D'[0]' -stim_base 5 -stim_label 5 roll \
-stim_file 6 ${subfolder}/${subject}/${subject}.${results}/motion_demean_FNIRT_3.5.1D'[1]' -stim_base 6 -stim_label 6 pitch \
-stim_file 7 ${subfolder}/${subject}/${subject}.${results}/motion_demean_FNIRT_3.5.1D'[2]' -stim_base 7 -stim_label 7 yaw \
-stim_file 8 ${subfolder}/${subject}/${subject}.${results}/motion_demean_FNIRT_3.5.1D'[3]' -stim_base 8 -stim_label 8 dS \
-stim_file 9 ${subfolder}/${subject}/${subject}.${results}/motion_demean_FNIRT_3.5.1D'[4]' -stim_base 9 -stim_label 9 dL \
-stim_file 10 ${subfolder}/${subject}/${subject}.${results}/motion_demean_FNIRT_3.5.1D'[5]' -stim_base 10 -stim_label 10 dP \
-iresp 1 ${subfolder}/${subject}/${subject}.${results}/iresp_CSaACQ.${subject}.nii \
-iresp 2 ${subfolder}/${subject}/${subject}.${results}/iresp_CSbACQ.${subject}.nii \
-iresp 3 ${subfolder}/${subject}/${subject}.${results}/iresp_CSaEXT.${subject}.nii \
-iresp 4 ${subfolder}/${subject}/${subject}.${results}/iresp_CSbEXT.${subject}.nii \
-gltsym 'SYM: +CSaACQ -CSbACQ' \
-glt_label 1 CSaACQvsCSbACQ \
-gltsym 'SYM: +CSaEXT -CSbEXT' \
-glt_label 2 CSaEXTvsCSbEXT \
-gltsym 'SYM: +CSaACQ -CSaEXT' \
-glt_label 3 CSaACQvsCSaEXT \
-gltsym 'SYM: +CSbACQ -CSbEXT' \
-glt_label 4 CSbACQvsCSbEXT \
-fout -tout -x1D ${subfolder}/${subject}/${subject}.${results}/X.xmat_FNIRT_3.5.1D -xjpeg ${subfolder}/${subject}/${subject}.${results}/X_FNIRT_3.5.jpg \
-x1D_uncensored ${subfolder}/${subject}/${subject}.${results}/X.nocensor.xmat_FNIRT_3.5.1D \
-fitts ${subfolder}/${subject}/${subject}.${results}/fitts.${subject}_FNIRT_3.5.nii \
-errts ${subfolder}/${subject}/${subject}.${results}/errts.${subject}_FNIRT_3.5.nii \
-bucket ${subfolder}/${subject}/${subject}.${results}/stats.${subject}_FNIRT_3.5.nii
Thanks!
Emily
