The proc.py command that generated the preprocessing and original GLM script:
# ==========================================================================
# script generated by the command:
#
# afni_proc.py -subj_id {$subj} -script proc.{$subj} -scr_overwrite -blocks \
# tshift align tlrc volreg blur mask scale regress -copy_anat \
# /home/shaw-raid2/3T/CAD/{$subj}/nii/T1_unifized.nii.gz \
# -tcat_remove_first_trs 0 -dsets \
# /home/shaw-raid2/3T/CAD/{$subj}/nii/tfMRIMID1PA.nii \
# /home/shaw-raid2/3T/CAD/{$subj}/nii/tfMRIMID2PA.nii -tlrc_base \
# MNI_avg152T1+tlrc -volreg_align_to first -volreg_align_e2a \
# -volreg_tlrc_warp -blip_reverse_dset \
# /home/shaw-raid2/3T/CAD/{$subj}/nii/rfMRIRESTAP.nii.gz -blur_size \
# 3.0 -regress_stim_times \
# /home/shaw-raid2/3T/CAD/{$subj}/1D/{$subj}expect0En.1D \
# /home/shaw-raid2/3T/CAD/{$subj}/1D/{$subj}expect0p.1D \
# /home/shaw-raid2/3T/CAD/{$subj}/1D/{$subj}expect2E.1D \
# /home/shaw-raid2/3T/CAD/{$subj}/1D/{$subj}expect40C.1D \
# /home/shaw-raid2/3T/CAD/{$subj}/1D/{$subj}expectm1E.1D \
# /home/shaw-raid2/3T/CAD/{$subj}/1D/{$subj}expectm20C.1D \
# /home/shaw-raid2/3T/CAD/{$subj}/1D/{$subj}fehler.1D \
# /home/shaw-raid2/3T/CAD/{$subj}/1D/{$subj}out0En.1D \
# /home/shaw-raid2/3T/CAD/{$subj}/1D/{$subj}out0Ep.1D \
# /home/shaw-raid2/3T/CAD/{$subj}/1D/{$subj}out2E.1D \
# /home/shaw-raid2/3T/CAD/{$subj}/1D/{$subj}out40C.1D \
# /home/shaw-raid2/3T/CAD/{$subj}/1D/{$subj}outm1E.1D \
# /home/shaw-raid2/3T/CAD/{$subj}/1D/{$subj}outm20C.1D \
# /home/shaw-raid2/3T/CAD/{$subj}/1D/{$subj}target.1D \
# -regress_stim_labels expect0En expect0p expect2E expect40C expectm1E \
# expectm20C fehler out0En out0Ep out2E out40C outm1E outm20C target \
# -regress_basis GAM -regress_censor_motion 0.5 -regress_make_ideal_sum \
# sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts
Then the GLM was rerun with -stim_times_IM to get the beta series. Correlations with the seed were computed for two conditions and Fisher z transformed.
set subj = $argv
cd $subj.results.pcb
# run the regression analysis
3dDeconvolve -input pb05.$subj.r*.scale+tlrc.HEAD \
-censor motion_${subj}_censor.1D \
-polort 6 -float \
-num_stimts 20 \
-stim_times_IM 1 stimuli2/{$subj}expect0En.1D 'GAM' \
-stim_label 1 expect0En \
-stim_times_IM 2 stimuli2/{$subj}expect0p.1D 'GAM' \
-stim_label 2 expect0p \
-stim_times_IM 3 stimuli2/{$subj}expect2E.1D 'GAM' \
-stim_label 3 expect2E \
-stim_times 4 stimuli2/{$subj}expect40C.1D 'GAM' \
-stim_label 4 expect40C \
-stim_times_IM 5 stimuli2/{$subj}expectm1E.1D 'GAM' \
-stim_label 5 expectm1E \
-stim_times 6 stimuli2/{$subj}expectm20C.1D 'GAM' \
-stim_label 6 expectm20C \
-stim_times 7 stimuli2/{$subj}fehler.1D 'GAM' \
-stim_label 7 fehler \
-stim_times_IM 8 stimuli2/{$subj}out0En.1D 'GAM' \
-stim_label 8 out0En \
-stim_times_IM 9 stimuli2/{$subj}out0Ep.1D 'GAM' \
-stim_label 9 out0Ep \
-stim_times_IM 10 stimuli2/{$subj}out2E_beta.1D 'GAM' \
-stim_label 10 out2E \
-stim_times 11 stimuli2/{$subj}out40C_beta.1D 'GAM' \
-stim_label 11 out40C \
-stim_times_IM 12 stimuli2/{$subj}outm1E_beta.1D 'GAM' \
-stim_label 12 outm1E \
-stim_times 13 stimuli2/{$subj}outm20C_beta.1D 'GAM' \
-stim_label 13 outm20C \
-stim_times 14 stimuli2/{$subj}target.1D 'GAM' \
-stim_label 14 target \
-stim_file 15 motion_demean.1D'[0]' -stim_base 15 -stim_label 15 roll \
-stim_file 16 motion_demean.1D'[1]' -stim_base 16 -stim_label 16 pitch \
-stim_file 17 motion_demean.1D'[2]' -stim_base 17 -stim_label 17 yaw \
-stim_file 18 motion_demean.1D'[3]' -stim_base 18 -stim_label 18 dS \
-stim_file 19 motion_demean.1D'[4]' -stim_base 19 -stim_label 19 dL \
-stim_file 20 motion_demean.1D'[5]' -stim_base 20 -stim_label 20 dP \
-fout -tout -x1D X.xmat.1D -xjpeg X.jpg \
-x1D_uncensored X.nocensor.xmat.1D \
-GOFORIT 6 \
-fitts fitts_beta_series2.$subj \
-errts errts_beta_series2.${subj} \
-bucket stats_beta_series2.$subj
3dbucket -prefix betas_expect_2 stats_beta_series2.{$subj}+tlrc.'[83..137(2)]'
3dbucket -prefix betas_expect_0 stats_beta_series2.{$subj}+tlrc.'[1..80(2)]'
3drefit -TR 0.8 betas_expect_2+tlrc
3drefit -TR 0.8 betas_expect_0+tlrc
3dmaskave -mask ../caudate_MNI_ROI+tlrc -quiet -mrange 1 1 betas_expect_2+tlrc. > caudate_expect_2_seed.1D
3dmaskave -mask ../caudate_MNI_ROI+tlrc -quiet -mrange 1 1 betas_expect_0+tlrc. > caudate_expect_0_seed.1D
3dfim+ -input betas_expect_2+tlrc. -polort 1 -ideal_file caudate_expect_2_seed.1D -out Correlation -bucket caudate_expect2_Correlation
3dfim+ -input betas_expect_0+tlrc. -polort 1 -ideal_file caudate_expect_0_seed.1D -out Correlation -bucket caudate_expect0_Correlation
3dcalc -prefix caudate_expect2_fisherz -a caudate_expect2_Correlation+tlrc. -expr 'log((1+a)/(1-a))/2'
3dcalc -prefix caudate_expect0_fisherz -a caudate_expect0_Correlation+tlrc. -expr 'log((1+a)/(1-a))/2'
cd ../
end
The t-tests compared patients and controls on difference scores.
cd {$subj}.results.pcb
echo $subj
3dcalc -overwrite -prefix expect2_minus_expect0 -a caudate_expect2_fisherz+tlrc -b caudate_expect0_fisherz+tlrc -expr 'a-b'
cd ../
end
There was much more activation for each group separately than for the difference between groups, so it was easier to convey the apparent lack of smoothness if I just showed the activation for the controls.
Here's the 3dttest++ command.
#!/bin/tcsh -xef
# created by uber_ttest.py: version 1.1 (October 18, 2012)
# creation date: Wed Feb 9 15:22:36 2022
# ---------------------- set process variables ----------------------
set mask_dset = /home/jaco-raid2/data/CAD/MID_analysis/new_good_preproc/old_masks_ANOVAS_etc_b4_consensus/90per_mask+tlrc
set dirA = /home/jaco-raid9/data/MID_analysis
set dirB = /home/jaco-raid2/data/CAD/MID_analysis/new_good_preproc
# specify and possibly create results directory
set results_dir = test.results
if ( ! -d $results_dir ) mkdir $results_dir
# ------------------------- process the data -------------------------
3dttest++ -prefix $results_dir/stats.ttest -AminusB \
-mask $mask_dset \
-clustsim \
-setA controls \
05782 "$dirA/P1005782.results.pcb/expect2_minus_expect0+tlrc[0]" \
06162 "$dirA/P1006162.results.pcb/expect2_minus_expect0+tlrc[0]" \
06397 "$dirA/P1006397.results.pcb/expect2_minus_expect0+tlrc[0]" \
06912 "$dirA/P1006912.results.pcb/expect2_minus_expect0+tlrc[0]" \
07161 "$dirA/P1007161.results.pcb/expect2_minus_expect0+tlrc[0]" \
07372 "$dirA/P1007372.results.pcb/expect2_minus_expect0+tlrc[0]" \
07451 "$dirA/P1007451.results.pcb/expect2_minus_expect0+tlrc[0]" \
07591 "$dirA/P1007591.results.pcb/expect2_minus_expect0+tlrc[0]" \
07601 "$dirA/P1007601.results.pcb/expect2_minus_expect0+tlrc[0]" \
10023 "$dirA/P1010023.results.pcb/expect2_minus_expect0+tlrc[0]" \
10053 "$dirA/P1010053.results.pcb/expect2_minus_expect0+tlrc[0]" \
10063 "$dirA/P1010063.results.pcb/expect2_minus_expect0+tlrc[0]" \
10083 "$dirA/P1010083.results.pcb/expect2_minus_expect0+tlrc[0]" \
10098 "$dirA/P1010098.results.pcb/expect2_minus_expect0+tlrc[0]" \
10103 "$dirA/P1010103.results.pcb/expect2_minus_expect0+tlrc[0]" \
10133 "$dirA/P1010133.results.pcb/expect2_minus_expect0+tlrc[0]" \
10143 "$dirA/P1010143.results.pcb/expect2_minus_expect0+tlrc[0]" \
10153 "$dirA/P1010153.results.pcb/expect2_minus_expect0+tlrc[0]" \
10163 "$dirA/P1010163.results.pcb/expect2_minus_expect0+tlrc[0]" \
10183 "$dirA/P1010183.results.pcb/expect2_minus_expect0+tlrc[0]" \
10208 "$dirA/P1010208.results.pcb/expect2_minus_expect0+tlrc[0]" \
10213 "$dirA/P1010213.results.pcb/expect2_minus_expect0+tlrc[0]" \
10228 "$dirA/P1010228.results.pcb/expect2_minus_expect0+tlrc[0]" \
10242 "$dirA/P1010242.results.pcb/expect2_minus_expect0+tlrc[0]" \
10278 "$dirA/P1010278.results.pcb/expect2_minus_expect0+tlrc[0]" \
10283 "$dirA/P1010283.results.pcb/expect2_minus_expect0+tlrc[0]" \
10299 "$dirA/P1010299.results.pcb/expect2_minus_expect0+tlrc[0]" \
10309 "$dirA/P1010309.results.pcb/expect2_minus_expect0+tlrc[0]" \
10407 "$dirA/P1010407.results.pcb/expect2_minus_expect0+tlrc[0]" \
10422 "$dirA/P1010422.results.pcb/expect2_minus_expect0+tlrc[0]" \
10519 "$dirA/P1010519.results.pcb/expect2_minus_expect0+tlrc[0]" \
10859 "$dirA/P1010859.results.pcb/expect2_minus_expect0+tlrc[0]" \
11033 "$dirA/P1011033.results.pcb/expect2_minus_expect0+tlrc[0]" \
11129 "$dirA/P1011129.results.pcb/expect2_minus_expect0+tlrc[0]" \
11139 "$dirA/P1011139.results.pcb/expect2_minus_expect0+tlrc[0]" \
11169 "$dirA/P1011169.results.pcb/expect2_minus_expect0+tlrc[0]" \
11399 "$dirA/P1011399.results.pcb/expect2_minus_expect0+tlrc[0]" \
11532 "$dirA/P1011532.results.pcb/expect2_minus_expect0+tlrc[0]" \
11852 "$dirA/P1011852.results.pcb/expect2_minus_expect0+tlrc[0]" \
11968 "$dirA/P1011968.results.pcb/expect2_minus_expect0+tlrc[0]" \
12033 "$dirA/P1012033.results.pcb/expect2_minus_expect0+tlrc[0]" \
12209 "$dirA/P1012209.results.pcb/expect2_minus_expect0+tlrc[0]" \
12219 "$dirA/P1012219.results.pcb/expect2_minus_expect0+tlrc[0]" \
12249 "$dirA/P1012249.results.pcb/expect2_minus_expect0+tlrc[0]" \
12259 "$dirA/P1012259.results.pcb/expect2_minus_expect0+tlrc[0]" \
12269 "$dirA/P1012269.results.pcb/expect2_minus_expect0+tlrc[0]" \
12333 "$dirA/P1012333.results.pcb/expect2_minus_expect0+tlrc[0]" \
12343 "$dirA/P1012343.results.pcb/expect2_minus_expect0+tlrc[0]" \
15038 "$dirA/P1015038.results.pcb/expect2_minus_expect0+tlrc[0]" \
-setB probands \
2104777 \
"$dirB/P2104777.results.pcb/expect2_minus_expect0+tlrc[0]" \
2110417 \
"$dirB/P2110417.results.pcb/expect2_minus_expect0+tlrc[0]" \
2110451 \
"$dirB/P2110451.results.pcb/expect2_minus_expect0+tlrc[0]" \
2110465 \
"$dirB/P2110465.results.pcb/expect2_minus_expect0+tlrc[0]" \
2110686 \
"$dirB/P2110686.results.pcb/expect2_minus_expect0+tlrc[0]" \
2110786 \
"$dirB/P2110786.results.pcb/expect2_minus_expect0+tlrc[0]" \
2111147 \
"$dirB/P2111147.results.pcb/expect2_minus_expect0+tlrc[0]" \
2111227 \
"$dirB/P2111227.results.pcb/expect2_minus_expect0+tlrc[0]" \
2111257 \
"$dirB/P2111257.results.pcb/expect2_minus_expect0+tlrc[0]" \
2111265 \
"$dirB/P2111265.results.pcb/expect2_minus_expect0+tlrc[0]" \
2111367 \
"$dirB/P2111367.results.pcb/expect2_minus_expect0+tlrc[0]" \
2111522 \
"$dirB/P2111522.results.pcb/expect2_minus_expect0+tlrc[0]" \
2111887 \
"$dirB/P2111887.results.pcb/expect2_minus_expect0+tlrc[0]" \
2111899 \
"$dirB/P2111899.results.pcb/expect2_minus_expect0+tlrc[0]" \
2112024 \
"$dirB/P2112024.results.pcb/expect2_minus_expect0+tlrc[0]" \
2112232 \
"$dirB/P2112232.results.pcb/expect2_minus_expect0+tlrc[0]" \
2112274 \
"$dirB/P2112274.results.pcb/expect2_minus_expect0+tlrc[0]" \
2204002 \
"$dirB/P2204002.results.pcb/expect2_minus_expect0+tlrc[0]" \
2204172 \
"$dirB/P2204172.results.pcb/expect2_minus_expect0+tlrc[0]" \
2210347 \
"$dirB/P2210347.results.pcb/expect2_minus_expect0+tlrc[0]" \
2210883 \
"$dirB/P2210883.results.pcb/expect2_minus_expect0+tlrc[0]" \
2211147 \
"$dirB/P2211147.results.pcb/expect2_minus_expect0+tlrc[0]" \
2211887 \
"$dirB/P2211887.results.pcb/expect2_minus_expect0+tlrc[0]" \
2211899 \
"$dirB/P2211899.results.pcb/expect2_minus_expect0+tlrc[0]" \
2212024 \
"$dirB/P2212024.results.pcb/expect2_minus_expect0+tlrc[0]" \
2212274 \
"$dirB/P2212274.results.pcb/expect2_minus_expect0+tlrc[0]" \
2212284 \
"$dirB/P2212284.results.pcb/expect2_minus_expect0+tlrc[0]" \
3101922 \
"$dirB/P3101922.results.pcb/expect2_minus_expect0+tlrc[0]" \
3102042 \
"$dirB/P3102042.results.pcb/expect2_minus_expect0+tlrc[0]" \
3102476 \
"$dirB/P3102476.results.pcb/expect2_minus_expect0+tlrc[0]" \
3103732 \
"$dirB/P3103732.results.pcb/expect2_minus_expect0+tlrc[0]" \
3103971 \
"$dirB/P3103971.results.pcb/expect2_minus_expect0+tlrc[0]" \
3104031 \
"$dirB/P3104031.results.pcb/expect2_minus_expect0+tlrc[0]" \
3104042 \
"$dirB/P3104042.results.pcb/expect2_minus_expect0+tlrc[0]" \
3104062 \
"$dirB/P3104062.results.pcb/expect2_minus_expect0+tlrc[0]" \
3104172 \
"$dirB/P3104172.results.pcb/expect2_minus_expect0+tlrc[0]" \
3104663 \
"$dirB/P3104663.results.pcb/expect2_minus_expect0+tlrc[0]" \
3110387 \
"$dirB/P3110387.results.pcb/expect2_minus_expect0+tlrc[0]" \
3110692 \
"$dirB/P3110692.results.pcb/expect2_minus_expect0+tlrc[0]" \
3110883 \
"$dirB/P3110883.results.pcb/expect2_minus_expect0+tlrc[0]" \
3110956 \
"$dirB/P3110956.results.pcb/expect2_minus_expect0+tlrc[0]" \
3111176 \
"$dirB/P3111176.results.pcb/expect2_minus_expect0+tlrc[0]" \
3111247 \
"$dirB/P3111247.results.pcb/expect2_minus_expect0+tlrc[0]" \
3111282 \
"$dirB/P3111282.results.pcb/expect2_minus_expect0+tlrc[0]" \
3111367 \
"$dirB/P3111367.results.pcb/expect2_minus_expect0+tlrc[0]" \
3111427 \
"$dirB/P3111427.results.pcb/expect2_minus_expect0+tlrc[0]" \
3111637 \
"$dirB/P3111637.results.pcb/expect2_minus_expect0+tlrc[0]" \
3111887 \
"$dirB/P3111887.results.pcb/expect2_minus_expect0+tlrc[0]" \
3111899 \
"$dirB/P3111899.results.pcb/expect2_minus_expect0+tlrc[0]" \
3112322 \
"$dirB/P3112322.results.pcb/expect2_minus_expect0+tlrc[0]" \
3200755 \
"$dirB/P3200755.results.pcb/expect2_minus_expect0+tlrc[0]" \
3210962 \
"$dirB/P3210962.results.pcb/expect2_minus_expect0+tlrc[0]" \
3211899 \
"$dirB/P3211899.results.pcb/expect2_minus_expect0+tlrc[0]" \
3300833 \
"$dirB/P3300833.results.pcb/expect2_minus_expect0+tlrc[0]" \
3400685 \
"$dirB/P3400685.results.pcb/expect2_minus_expect0+tlrc[0]" \
4100631 \
"$dirB/P4100631.results.pcb/expect2_minus_expect0+tlrc[0]" \
4100833 \
"$dirB/P4100833.results.pcb/expect2_minus_expect0+tlrc[0]" \
4102082 \
"$dirB/P4102082.results.pcb/expect2_minus_expect0+tlrc[0]" \
4102273 \
"$dirB/P4102273.results.pcb/expect2_minus_expect0+tlrc[0]" \
4103882 \
"$dirB/P4103882.results.pcb/expect2_minus_expect0+tlrc[0]" \
4104604 \
"$dirB/P4104604.results.pcb/expect2_minus_expect0+tlrc[0]" \
4104647 \
"$dirB/P4104647.results.pcb/expect2_minus_expect0+tlrc[0]" \
4110363 \
"$dirB/P4110363.results.pcb/expect2_minus_expect0+tlrc[0]" \
4110632 \
"$dirB/P4110632.results.pcb/expect2_minus_expect0+tlrc[0]" \
4111147 \
"$dirB/P4111147.results.pcb/expect2_minus_expect0+tlrc[0]" \
4111257 \
"$dirB/P4111257.results.pcb/expect2_minus_expect0+tlrc[0]" \
4111367 \
"$dirB/P4111367.results.pcb/expect2_minus_expect0+tlrc[0]" \
4111457 \
"$dirB/P4111457.results.pcb/expect2_minus_expect0+tlrc[0]" \
4111522 \
"$dirB/P4111522.results.pcb/expect2_minus_expect0+tlrc[0]" \
4111777 \
"$dirB/P4111777.results.pcb/expect2_minus_expect0+tlrc[0]" \
4112024 \
"$dirB/P4112024.results.pcb/expect2_minus_expect0+tlrc[0]" \
4112222 \
"$dirB/P4112222.results.pcb/expect2_minus_expect0+tlrc[0]" \
4112232 \
"$dirB/P4112232.results.pcb/expect2_minus_expect0+tlrc[0]" \
4203218 \
"$dirB/P4203218.results.pcb/expect2_minus_expect0+tlrc[0]" \
5102243 \
"$dirB/P5102243.results.pcb/expect2_minus_expect0+tlrc[0]" \
5104604 \
"$dirB/P5104604.results.pcb/expect2_minus_expect0+tlrc[0]" \
5110387 \
"$dirB/P5110387.results.pcb/expect2_minus_expect0+tlrc[0]" \
5110646 \
"$dirB/P5110646.results.pcb/expect2_minus_expect0+tlrc[0]" \
5110867 \
"$dirB/P5110867.results.pcb/expect2_minus_expect0+tlrc[0]" \
5204604 \
"$dirB/P5204604.results.pcb/expect2_minus_expect0+tlrc[0]" \
6000631 \
"$dirB/P6000631.results.pcb/expect2_minus_expect0+tlrc[0]" \
6001403 \
"$dirB/P6001403.results.pcb/expect2_minus_expect0+tlrc[0]" \
6001501 \
"$dirB/P6001501.results.pcb/expect2_minus_expect0+tlrc[0]" \
6002165 \
"$dirB/P6002165.results.pcb/expect2_minus_expect0+tlrc[0]" \
6002476 \
"$dirB/P6002476.results.pcb/expect2_minus_expect0+tlrc[0]" \
6002663 \
"$dirB/P6002663.results.pcb/expect2_minus_expect0+tlrc[0]" \
6002733 \
"$dirB/P6002733.results.pcb/expect2_minus_expect0+tlrc[0]" \
6002901 \
"$dirB/P6002901.results.pcb/expect2_minus_expect0+tlrc[0]" \
6003622 \
"$dirB/P6003622.results.pcb/expect2_minus_expect0+tlrc[0]" \
6003691 \
"$dirB/P6003691.results.pcb/expect2_minus_expect0+tlrc[0]" \
6003762 \
"$dirB/P6003762.results.pcb/expect2_minus_expect0+tlrc[0]" \
6003851 \
"$dirB/P6003851.results.pcb/expect2_minus_expect0+tlrc[0]" \
6003961 \
"$dirB/P6003961.results.pcb/expect2_minus_expect0+tlrc[0]" \
6003992 \
"$dirB/P6003992.results.pcb/expect2_minus_expect0+tlrc[0]" \
6004002 \
"$dirB/P6004002.results.pcb/expect2_minus_expect0+tlrc[0]" \
6004011 \
"$dirB/P6004011.results.pcb/expect2_minus_expect0+tlrc[0]" \
6004071 \
"$dirB/P6004071.results.pcb/expect2_minus_expect0+tlrc[0]" \
6004172 \
"$dirB/P6004172.results.pcb/expect2_minus_expect0+tlrc[0]" \
6004181 \
"$dirB/P6004181.results.pcb/expect2_minus_expect0+tlrc[0]" \
6004202 \
"$dirB/P6004202.results.pcb/expect2_minus_expect0+tlrc[0]" \
6004213 \
"$dirB/P6004213.results.pcb/expect2_minus_expect0+tlrc[0]" \
6004231 \
"$dirB/P6004231.results.pcb/expect2_minus_expect0+tlrc[0]" \
6004604 \
"$dirB/P6004604.results.pcb/expect2_minus_expect0+tlrc[0]" \
6004623 \
"$dirB/P6004623.results.pcb/expect2_minus_expect0+tlrc[0]" \
6004647 \
"$dirB/P6004647.results.pcb/expect2_minus_expect0+tlrc[0]" \
6004654 \
"$dirB/P6004654.results.pcb/expect2_minus_expect0+tlrc[0]" \
6004663 \
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