Thank you for helping me understand some of the differences between FSL and AFNI and giving me the recommended way of using AFNI in this context. For clarity, the actual changes I am making to my code is switching from 3dBandpass to 3dTProject, and changing the polort option in 3dDeconvolve to 0 since I'm already bandpassing. However, I'm not exactly sure how I am supposed to implement the following sentence in my code: "The closest analogy to FSL that I would recommend in AFNI would be to eschew the polynomial regressors in AFNI and instead put in trigonometric regressors to pick up the low frequencies you want filtered out, and let the linear regression + pre-whitening model do it all at once." So by eschewing polynomial regressors you mean to change the polort option to 0, correct? But I do not understand how to put in trigonometric regressors to pick up the low frequencies. Is that what 3dTProject accomplishes?

Again, thank you for advising me. My new 3dDeconvolve command is this:

3dDeconvolve -input ${FLANKER_NIFTI} \
-nfirst 0 \
-polort 0 \
-num_stimts 10 \
-basis_normall 1 \
-mask ${outDir}/mask/*_mask.nii.gz \
-stim_times 1 ${timing_array[0]} 'GAM(6.0024,0.9996)' -stim_label 1 con \
-stim_times 2 ${timing_array[1]} 'GAM(6.0024,0.9996)' -stim_label 2 errors \
-stim_times 3 ${timing_array[2]} 'GAM(6.0024,0.9996)' -stim_label 3 inc \
-stim_times 4 ${timing_array[3]} 'GAM(6.0024,0.9996)' -stim_label 4 neu \
-stim_file 5 ${motion_file}[0] -stim_label 5 roll \
-stim_file 6 ${motion_file}[1] -stim_label 6 pitch \
-stim_file 7 ${motion_file}[2] -stim_label 7 yaw \
-stim_file 8 ${motion_file}[3] -stim_label 8 I_S \
-stim_file 9 ${motion_file}[4] -stim_label 9 R_L \
-stim_file 10 ${motion_file}[5] -stim_label 10 A_P \
-num_glt 7 \
-glt_label 1 con_ave -gltsym 'SYM: con' \
-glt_label 2 errors_ave -gltsym 'SYM: errors' \
-glt_label 3 inc_ave -gltsym 'SYM: inc' \
-glt_label 4 neu_ave -gltsym 'SYM: neu' \
-glt_label 5 con-neu -gltsym 'SYM: +con -neu' \
-glt_label 6 inc-neu -gltsym 'SYM: +inc -neu' \
-glt_label 7 con-inc -gltsym 'SYM: +con -inc' \
-tout -fout -bucket sub${subNum}_bucket -xjpeg sub${subNum}_glm_matrix.jpg -x1D_stop &&\
3dREMLfit -matrix sub${subNum}_bucket.xmat.1D \
-input ${FLANKER_NIFTI} \
-mask ${outDir}/mask/*_mask.nii.gz \
-fout -tout -Rbuck sub${subNum}_bucket_REML -Rvar sub${subNum}_bucket_REMLvar -verb