I have used gltsym before for contrasts but for reasons I don’t understand (I thought it was a white space error or something) when it plug it into the afni proc the gltsym in the tcsh is all over the place for example ’ separating parts of my titles. I ended up fixing the gltsym part of 3dDeconvolve on my own but I get command not found errors for gltsym. Below is an example of what I put into the afni proc. Note: I have changed labels and paths in order to save space. If you want the original text I can send it to you via email.
Thanks for your help
afni_proc.py
-subj_id TestofTent${subject}_${runname}
-copy_anat /Users/jd/testoftent/anat/struc1_e1.nii
-dsets /Users/jd/testoftent/func/func?.nii
-blocks despike align volreg blur mask scale regress
-script Testoftent_Contrast.tcsh
-volreg_align_to MIN_OUTLIER
-volreg_align_e2a
-volreg_allin_cost lpa+zz
-volreg_post_vr_allin yes
-volreg_pvra_base_index MIN_OUTLIER
-align_opts_aea -AddEdge -giant_move
-blur_size 4
-regress_stim_times /Users/jd/testoftent/stimuli/.txt
-regress_stim_labels p1 p2 p3 p4 p5 p6 p7 p8 p9 p10 p11 p12
-regress_basis_multi ‘TENT(0,17.6,16)’ ‘TENT(0,17.6,16)’ ‘TENT(0,17.6,16)’ ‘TENT(0,17.6,16)’ ‘TENT(0,17.6,16)’ ‘BLOCK(64.9,1)’ ‘TENT(0,17.6,16)’ ‘TENT(0,17.6,16)’ ‘TENT(0,17.6,16)’ ‘TENT(0,17.6,16)’ ‘BLOCK(64.9,1)’ ‘TENT(0,17.6,16)’
-regress_local_times
-regress_censor_motion 0.3
-regress_motion_per_run
-regress_opts_3dD
-gltsym 'SYM: +.083p1 +.083p2 +.083p3 +.083p4 +.083p5 +.083p6 +.083p7 +.083p8 +.083p9 +.083p10 +.083p11 +.083p12’
-glt_label 1 a
-gltsym 'SYM: +.25p3 +.25p4 +.25p9 +.25p12’
-glt_label 2 b
-gltsym 'SYM: +.5p2 +.5p8’
-glt_label 3 c
-gltsym 'SYM: +.5p6 +.5p11’
-glt_label 4 d
-gltsym 'SYM: +.25p1 +.25p5 +.25p7 +.25p10’
-glt_label 5 e
-gltsym 'SYM: +.167p1 +.167p2 +.167p3 +.167p4 +.167p5 +.167p6’
-glt_label 6 f
-gltsym 'SYM: +.167p7 +.167p8 +.167p9 +.167p10 +.167p11 +.167p12’
-glt_label 7 g
-gltsym 'SYM: +.5p3 +.5p4’
-glt_label 8 h
-gltsym 'SYM: +.5p9 +.5p12’
-glt_label 9 i
-gltsym 'SYM: +.5p1 +.5p5’
-glt_label 10 j
-gltsym 'SYM: +.5p7 +.5p10’
-glt_label 11 k
-gltsym 'SYM: +.5p2 -.25p3 -.25p4 +.5p8 -.25p9 -.25*p12’
-glt_label 12 l
-float
-jobs 4
-regress_est_blur_epits
-regress_est_blur_errts
-regress_run_clustsim no
-bash