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: +.083*p1 +.083

*p2 +.083*p3 +.083

*p4 +.083*p5 +.083

*p6 +.083*p7 +.083

*p8 +.083*p9 +.083

*p10 +.083*p11 +.083

*p12’*

-glt_label 1 a

-gltsym 'SYM: +.25p3 +.25

-glt_label 1 a

-gltsym 'SYM: +.25

*p4 +.25*p9 +.25

*p12’*

-glt_label 2 b

-gltsym 'SYM: +.5p2 +.5

-glt_label 2 b

-gltsym 'SYM: +.5

*p8’*

-glt_label 3 c

-gltsym 'SYM: +.5p6 +.5

-glt_label 3 c

-gltsym 'SYM: +.5

*p11’*

-glt_label 4 d

-gltsym 'SYM: +.25p1 +.25

-glt_label 4 d

-gltsym 'SYM: +.25

*p5 +.25*p7 +.25

*p10’*

-glt_label 5 e

-gltsym 'SYM: +.167p1 +.167

-glt_label 5 e

-gltsym 'SYM: +.167

*p2 +.167*p3 +.167

*p4 +.167*p5 +.167

*p6’*

-glt_label 6 f

-gltsym 'SYM: +.167p7 +.167

-glt_label 6 f

-gltsym 'SYM: +.167

*p8 +.167*p9 +.167

*p10 +.167*p11 +.167

*p12’*

-glt_label 7 g

-gltsym 'SYM: +.5p3 +.5

-glt_label 7 g

-gltsym 'SYM: +.5

*p4’*

-glt_label 8 h

-gltsym 'SYM: +.5p9 +.5

-glt_label 8 h

-gltsym 'SYM: +.5

*p12’*

-glt_label 9 i

-gltsym 'SYM: +.5p1 +.5

-glt_label 9 i

-gltsym 'SYM: +.5

*p5’*

-glt_label 10 j

-gltsym 'SYM: +.5p7 +.5

-glt_label 10 j

-gltsym 'SYM: +.5

*p10’*

-glt_label 11 k

-gltsym 'SYM: +.5p2 -.25

-glt_label 11 k

-gltsym 'SYM: +.5

*p3 -.25*p4 +.5

*p8 -.25*p9 -.25*p12’

-glt_label 12 l

-float

-jobs 4

-regress_est_blur_epits

-regress_est_blur_errts

-regress_run_clustsim no

-bash