issue with running t-test in afni

Hi everyone,
I am working on an emotional go/no-go scanning paradigm. We are interested in brain activity during correct responses to go and no-go stimuli as well as brain activity during omission and commission errors. To accomplish this goal I made vectors for correct go, correct no-go, omission and commission errors for each emotion we studied (happy, angry, fear, and a black box control).
However, this setup has some issues with subjects who scored perfectly or got a score of 0 on one of the tasks would be missing a vector (since they either had no accurate responses for a given emotion and go/no-go state or would have either no omission or no commission errors for a given emotion). To circumvent this problem, I tried to make ‘dummy vectors’ with timepoints which would then be censored that could ‘replace’ the missing vectors.
When I tried to run my data using this method we got errors while doing the t-test since there were too many censored-out vectors. The output that resulted didn’t make sense (ie there was no brain activation in controls even though I would expect to see some activation in controls during this paradigm). Please let me know if any of you have thoughts regarding how to proceed.

When I tried to run my data using this method we got errors while doing the t-test since there were too many censored-out vectors.

Are you talking about t-test at the subject or group level? Could you show your script?

Hello,

Thank you for replying. I am working on a group level t-test.
The script is below. I have only included the first 5 subjects in each group due to space constraints.

cd /nfs/mint/results/gng/SubjectsFolders/Test_All_Subj

set output_dir = /nfs/mint/results/gng/SubjectsFolders/GroupAnalysis/Take2

#GO_ANGRY

set output = go_angry_gng

3dttest++ -prefix ${output_dir}/${output}

-setA TD

1 AH1346.results/stats.AH1346+tlrc.‘[1]’
2 AP1129.results/stats.AP1129+tlrc.‘[1]’
3 AR1342.results/stats.AR1342+tlrc.‘[1]’
4 BK1041.results/stats.BK1041+tlrc.‘[1]’
5 BK1268.results/stats.BK1268+tlrc.‘[1]’

-setB ADHD

49 AA1299.results/stats.AA1299+tlrc.‘[1]’
50 AD1173.results/stats.AD1173+tlrc.‘[1]’
51 AM1304.results/stats.AM1304+tlrc.‘[1]’
52 AM1319.results/stats.AM1319+tlrc.‘[1]’
53 AP1162.results/stats.AP1162+tlrc.‘[1]’
54 AS1001.results/stats.AS1001+tlrc.‘[1]’ \

3dcalc -a ${output_dir}/rsttest+tlrc. -b ${output_dir}/${output}+tlrc. -expr ‘ispositive(a)*b’ -prefix ${output_dir}/${output}_masked

#GO_ANGRY_OM

set output = go_angry_om_ttest_gng

3dttest++ -prefix ${output_dir}/${output}

-setA TD

1 AH1346.results/stats.AH1346+tlrc.‘[4]’
2 AP1129.results/stats.AP1129+tlrc.‘[4]’
3 AR1342.results/stats.AR1342+tlrc.‘[4]’
4 BK1041.results/stats.BK1041+tlrc.‘[4]’
5 BK1268.results/stats.BK1268+tlrc.‘[4]’

-setB ADHD

49 AA1299.results/stats.AA1299+tlrc.‘[4]’
50 AD1173.results/stats.AD1173+tlrc.‘[4]’
51 AM1304.results/stats.AM1304+tlrc.‘[4]’
52 AM1319.results/stats.AM1319+tlrc.‘[4]’
53 AP1162.results/stats.AP1162+tlrc.‘[4]’
54 AS1001.results/stats.AS1001+tlrc.‘[4]’ \

3dcalc -a ${output_dir}/rsttest+tlrc. -b ${output_dir}/${output}+tlrc. -expr ‘ispositive(a)*b’ -prefix ${output_dir}/${output}_masked

#No Go Angry

set output = nogo_angry_ttest_gng

3dttest++ -prefix ${output_dir}/${output}

-setA TD

1 AH1346.results/stats.AH1346+tlrc.‘[7]’
2 AP1129.results/stats.AP1129+tlrc.‘[7]’
3 AR1342.results/stats.AR1342+tlrc.‘[7]’
4 BK1041.results/stats.BK1041+tlrc.‘[7]’
5 BK1268.results/stats.BK1268+tlrc.‘[7]’ \


-setB ADHD

49 AA1299.results/stats.AA1299+tlrc.‘[7]’
50 AD1173.results/stats.AD1173+tlrc.‘[7]’
51 AM1304.results/stats.AM1304+tlrc.‘[7]’
52 AM1319.results/stats.AM1319+tlrc.‘[7]’
53 AP1162.results/stats.AP1162+tlrc.‘[7]’
54 AS1001.results/stats.AS1001+tlrc.‘[7]’
55 AS1017.results/stats.AS1017+tlrc.‘[7]’ \

3dcalc -a ${output_dir}/rsttest+tlrc. -b ${output_dir}/${output}+tlrc. -expr ‘ispositive(a)*b’ -prefix ${output_dir}/${output}_masked

#No Go Angry Comm

set output = nogo_angry_comm_ttest_gng

3dttest++ -prefix ${output_dir}/${output}

-setA TD

1 AH1346.results/stats.AH1346+tlrc.‘[10]’
2 AP1129.results/stats.AP1129+tlrc.‘[10]’
3 AR1342.results/stats.AR1342+tlrc.‘[10]’
4 BK1041.results/stats.BK1041+tlrc.‘[10]’
5 BK1268.results/stats.BK1268+tlrc.‘[10]’ \


-setB ADHD

49 AA1299.results/stats.AA1299+tlrc.‘[10]’
50 AD1173.results/stats.AD1173+tlrc.‘[10]’
51 AM1304.results/stats.AM1304+tlrc.‘[10]’
52 AM1319.results/stats.AM1319+tlrc.‘[10]’
53 AP1162.results/stats.AP1162+tlrc.‘[10]’
54 AS1001.results/stats.AS1001+tlrc.‘[10]’
55 AS1017.results/stats.AS1017+tlrc.‘[10]’ \

3dcalc -a ${output_dir}/rsttest+tlrc. -b ${output_dir}/${output}+tlrc. -expr ‘ispositive(a)*b’ -prefix ${output_dir}/${output}_masked

#Go Fear

set output = go_fear_ttest_gng

3dttest++ -prefix ${output_dir}/${output}

-setA TD

1 BK1268.results/stats.BK1268+tlrc.‘[13]’
1 AH1346.results/stats.AH1346+tlrc.‘[13]’
2 AP1129.results/stats.AP1129+tlrc.‘[13]’
3 AR1342.results/stats.AR1342+tlrc.‘[13]’
4 BK1041.results/stats.BK1041+tlrc.‘[13]’
5 BK1268.results/stats.BK1268+tlrc.‘[13]’

-setB ADHD

49 AA1299.results/stats.AA1299+tlrc.‘[13]’
50 AD1173.results/stats.AD1173+tlrc.‘[13]’
51 AM1304.results/stats.AM1304+tlrc.‘[13]’
52 AM1319.results/stats.AM1319+tlrc.‘[13]’
53 AP1162.results/stats.AP1162+tlrc.‘[13]’
54 AS1001.results/stats.AS1001+tlrc.‘[13]’
55 AS1017.results/stats.AS1017+tlrc.‘[13]’ \

3dcalc -a ${output_dir}/rsttest+tlrc. -b ${output_dir}/${output}+tlrc. -expr ‘ispositive(a)*b’ -prefix ${output_dir}/${output}_masked

#Go Fear Omission

set output = go_fear_om_ttest_gng

3dttest++ -prefix ${output_dir}/${output}

-setA TD

1 AH1346.results/stats.AH1346+tlrc.‘[16]’
2 AP1129.results/stats.AP1129+tlrc.‘[16]’
3 AR1342.results/stats.AR1342+tlrc.‘[16]’
4 BK1041.results/stats.BK1041+tlrc.‘[16]’
5 BK1268.results/stats.BK1268+tlrc.‘[16]’

-setB ADHD

49 AA1299.results/stats.AA1299+tlrc.‘[16]’
50 AD1173.results/stats.AD1173+tlrc.‘[16]’
51 AM1304.results/stats.AM1304+tlrc.‘[16]’
52 AM1319.results/stats.AM1319+tlrc.‘[16]’
53 AP1162.results/stats.AP1162+tlrc.‘[16]’
54 AS1001.results/stats.AS1001+tlrc.‘[16]’
55 AS1017.results/stats.AS1017+tlrc.‘[16]’ \

3dcalc -a ${output_dir}/rsttest+tlrc. -b ${output_dir}/${output}+tlrc. -expr ‘ispositive(a)*b’ -prefix ${output_dir}/${output}_masked

#No Go Fear

set output = nogo_fear_ttest_gng

3dttest++ -prefix ${output_dir}/${output}

-setA TD

1 AH1346.results/stats.AH1346+tlrc.‘[19]’
2 AP1129.results/stats.AP1129+tlrc.‘[19]’
3 AR1342.results/stats.AR1342+tlrc.‘[19]’
4 BK1041.results/stats.BK1041+tlrc.‘[19]’
5 BK1268.results/stats.BK1268+tlrc.‘[19]’ \


-setB ADHD

49 AA1299.results/stats.AA1299+tlrc.‘[19]’
50 AD1173.results/stats.AD1173+tlrc.‘[19]’
51 AM1304.results/stats.AM1304+tlrc.‘[19]’
52 AM1319.results/stats.AM1319+tlrc.‘[19]’
53 AP1162.results/stats.AP1162+tlrc.‘[19]’
54 AS1001.results/stats.AS1001+tlrc.‘[19]’
55 AS1017.results/stats.AS1017+tlrc.‘[19]’ \

3dcalc -a ${output_dir}/rsttest+tlrc. -b ${output_dir}/${output}+tlrc. -expr ‘ispositive(a)*b’ -prefix ${output_dir}/${output}_masked

#No Go Fear Comm

set output = nogo_fear_comm_ttest_gng

3dttest++ -prefix ${output_dir}/${output}

-setA TD

1 AH1346.results/stats.AH1346+tlrc.‘[22]’
2 AP1129.results/stats.AP1129+tlrc.‘[22]’
3 AR1342.results/stats.AR1342+tlrc.‘[22]’
4 BK1041.results/stats.BK1041+tlrc.‘[22]’
5 BK1268.results/stats.BK1268+tlrc.‘[22]’ \


-setB ADHD

49 AA1299.results/stats.AA1299+tlrc.‘[22]’
50 AD1173.results/stats.AD1173+tlrc.‘[22]’
51 AM1304.results/stats.AM1304+tlrc.‘[22]’
52 AM1319.results/stats.AM1319+tlrc.‘[22]’
53 AP1162.results/stats.AP1162+tlrc.‘[22]’
54 AS1001.results/stats.AS1001+tlrc.‘[22]’
55 AS1017.results/stats.AS1017+tlrc.‘[22]’ \

3dcalc -a ${output_dir}/rsttest+tlrc. -b ${output_dir}/${output}+tlrc. -expr ‘ispositive(a)*b’ -prefix ${output_dir}/${output}_masked

#Go Happy

set output = go_happy_ttest_gng

3dttest++ -prefix ${output_dir}/${output}

-setA TD

1 AH1346.results/stats.AH1346+tlrc.‘[25]’
2 AP1129.results/stats.AP1129+tlrc.‘[25]’
3 AR1342.results/stats.AR1342+tlrc.‘[25]’
4 BK1041.results/stats.BK1041+tlrc.‘[25]’
5 BK1268.results/stats.BK1268+tlrc.‘[25]’ \


-setB ADHD

49 AA1299.results/stats.AA1299+tlrc.‘[25]’
50 AD1173.results/stats.AD1173+tlrc.‘[25]’
51 AM1304.results/stats.AM1304+tlrc.‘[25]’
52 AM1319.results/stats.AM1319+tlrc.‘[25]’
53 AP1162.results/stats.AP1162+tlrc.‘[25]’
54 AS1001.results/stats.AS1001+tlrc.‘[25]’
55 AS1017.results/stats.AS1017+tlrc.‘[25]’ \

3dcalc -a ${output_dir}/rsttest+tlrc. -b ${output_dir}/${output}+tlrc. -expr ‘ispositive(a)*b’ -prefix ${output_dir}/${output}_masked

#Go Happy Omission

set output = go_happy_om_ttest_gng

3dttest++ -prefix ${output_dir}/${output}

-setA TD

1 BK1268.results/stats.BK1268+tlrc.‘[28]’
1 AH1346.results/stats.AH1346+tlrc.‘[28]’
2 AP1129.results/stats.AP1129+tlrc.‘[28]’
3 AR1342.results/stats.AR1342+tlrc.‘[28]’
4 BK1041.results/stats.BK1041+tlrc.‘[28]’
5 BK1268.results/stats.BK1268+tlrc.‘[28]’ \


-setB ADHD

49 AA1299.results/stats.AA1299+tlrc.‘[28]’
50 AD1173.results/stats.AD1173+tlrc.‘[28]’
51 AM1304.results/stats.AM1304+tlrc.‘[28]’
52 AM1319.results/stats.AM1319+tlrc.‘[28]’
53 AP1162.results/stats.AP1162+tlrc.‘[28]’
54 AS1001.results/stats.AS1001+tlrc.‘[28]’
55 AS1017.results/stats.AS1017+tlrc.‘[28]’ \

3dcalc -a ${output_dir}/rsttest+tlrc. -b ${output_dir}/${output}+tlrc. -expr ‘ispositive(a)*b’ -prefix ${output_dir}/${output}_masked

#No Go Happy

set output = nogo_happy_ttest_gng

3dttest++ -prefix ${output_dir}/${output}

-setA TD

1 AH1346.results/stats.AH1346+tlrc.‘[31]’
2 AP1129.results/stats.AP1129+tlrc.‘[31]’
3 AR1342.results/stats.AR1342+tlrc.‘[31]’
4 BK1041.results/stats.BK1041+tlrc.‘[31]’
5 BK1268.results/stats.BK1268+tlrc.‘[31]’

-setB ADHD

49 AA1299.results/stats.AA1299+tlrc.‘[31]’
50 AD1173.results/stats.AD1173+tlrc.‘[31]’
51 AM1304.results/stats.AM1304+tlrc.‘[31]’
52 AM1319.results/stats.AM1319+tlrc.‘[31]’
53 AP1162.results/stats.AP1162+tlrc.‘[31]’
54 AS1001.results/stats.AS1001+tlrc.‘[31]’
55 AS1017.results/stats.AS1017+tlrc.‘[31]’ \

3dcalc -a ${output_dir}/rsttest+tlrc. -b ${output_dir}/${output}+tlrc. -expr ‘ispositive(a)*b’ -prefix ${output_dir}/${output}_masked

#No Go Happy Comm

set output = nogo_happy_comm_ttest_gng

3dttest++ -prefix ${output_dir}/${output}

-setA TD

1 AH1346.results/stats.AH1346+tlrc.‘[34]’
2 AP1129.results/stats.AP1129+tlrc.‘[34]’
3 AR1342.results/stats.AR1342+tlrc.‘[34]’
4 BK1041.results/stats.BK1041+tlrc.‘[34]’
5 BK1268.results/stats.BK1268+tlrc.‘[34]’

-setB ADHD

49 AA1299.results/stats.AA1299+tlrc.‘[34]’
50 AD1173.results/stats.AD1173+tlrc.‘[34]’
51 AM1304.results/stats.AM1304+tlrc.‘[34]’
52 AM1319.results/stats.AM1319+tlrc.‘[34]’
53 AP1162.results/stats.AP1162+tlrc.‘[34]’
54 AS1001.results/stats.AS1001+tlrc.‘[34]’
55 AS1017.results/stats.AS1017+tlrc.‘[34]’ \

3dcalc -a ${output_dir}/rsttest+tlrc. -b ${output_dir}/${output}+tlrc. -expr ‘ispositive(a)*b’ -prefix ${output_dir}/${output}_masked

#Go Control

set output = go_control_ttest_gng

3dttest++ -prefix ${output_dir}/${output}

-setA TD

1 AH1346.results/stats.AH1346+tlrc.‘[37]’
2 AP1129.results/stats.AP1129+tlrc.‘[37]’
3 AR1342.results/stats.AR1342+tlrc.‘[37]’
4 BK1041.results/stats.BK1041+tlrc.‘[37]’
5 BK1268.results/stats.BK1268+tlrc.‘[37]’

-setB ADHD

49 AA1299.results/stats.AA1299+tlrc.‘[37]’
50 AD1173.results/stats.AD1173+tlrc.‘[37]’
51 AM1304.results/stats.AM1304+tlrc.‘[37]’
52 AM1319.results/stats.AM1319+tlrc.‘[37]’
53 AP1162.results/stats.AP1162+tlrc.‘[37]’
54 AS1001.results/stats.AS1001+tlrc.‘[37]’
55 AS1017.results/stats.AS1017+tlrc.‘[37]’ \

3dcalc -a ${output_dir}/rsttest+tlrc. -b ${output_dir}/${output}+tlrc. -expr ‘ispositive(a)*b’ -prefix ${output_dir}/${output}_masked

#Go Control Omission

set output = go_control_om_ttest_gng

3dttest++ -prefix ${output_dir}/${output}

-setA TD

1 AH1346.results/stats.AH1346+tlrc.‘[40]’
2 AP1129.results/stats.AP1129+tlrc.‘[40]’
3 AR1342.results/stats.AR1342+tlrc.‘[40]’
4 BK1041.results/stats.BK1041+tlrc.‘[40]’
5 BK1268.results/stats.BK1268+tlrc.‘[40]’

-setB ADHD

49 AA1299.results/stats.AA1299+tlrc.‘[40]’
50 AD1173.results/stats.AD1173+tlrc.‘[40]’
51 AM1304.results/stats.AM1304+tlrc.‘[40]’
52 AM1319.results/stats.AM1319+tlrc.‘[40]’
53 AP1162.results/stats.AP1162+tlrc.‘[40]’
54 AS1001.results/stats.AS1001+tlrc.‘[40]’
55 AS1017.results/stats.AS1017+tlrc.‘[40]’ \

3dcalc -a ${output_dir}/rsttest+tlrc. -b ${output_dir}/${output}+tlrc. -expr ‘ispositive(a)*b’ -prefix ${output_dir}/${output}_masked

#No Go Control

set output = nogo_control_ttest_gng

3dttest++ -prefix ${output_dir}/${output}

-setA TD

1 AH1346.results/stats.AH1346+tlrc.‘[43]’
2 AP1129.results/stats.AP1129+tlrc.‘[43]’
3 AR1342.results/stats.AR1342+tlrc.‘[43]’
4 BK1041.results/stats.BK1041+tlrc.‘[43]’
5 BK1268.results/stats.BK1268+tlrc.‘[43]’

-setB ADHD

49 AA1299.results/stats.AA1299+tlrc.‘[43]’
50 AD1173.results/stats.AD1173+tlrc.‘[43]’
51 AM1304.results/stats.AM1304+tlrc.‘[43]’
52 AM1319.results/stats.AM1319+tlrc.‘[43]’
53 AP1162.results/stats.AP1162+tlrc.‘[43]’
54 AS1001.results/stats.AS1001+tlrc.‘[43]’
55 AS1017.results/stats.AS1017+tlrc.‘[43]’ \

3dcalc -a ${output_dir}/rsttest+tlrc. -b ${output_dir}/${output}+tlrc. -expr ‘ispositive(a)*b’ -prefix ${output_dir}/${output}_masked

#No Go Control Comm

set output = nogo_control_comm_ttest_gng

3dttest++ -prefix ${output_dir}/${output}

-setA TD

1 AH1346.results/stats.AH1346+tlrc.‘[46]’
2 AP1129.results/stats.AP1129+tlrc.‘[46]’
3 AR1342.results/stats.AR1342+tlrc.‘[46]’
4 BK1041.results/stats.BK1041+tlrc.‘[46]’
5 BK1268.results/stats.BK1268+tlrc.‘[46]’

-setB ADHD

49 AA1299.results/stats.AA1299+tlrc.‘[46]’
50 AD1173.results/stats.AD1173+tlrc.‘[46]’
51 AM1304.results/stats.AM1304+tlrc.‘[46]’
52 AM1319.results/stats.AM1319+tlrc.‘[46]’
53 AP1162.results/stats.AP1162+tlrc.‘[46]’
54 AS1001.results/stats.AS1001+tlrc.‘[46]’
55 AS1017.results/stats.AS1017+tlrc.‘[46]’ \

3dcalc -a ${output_dir}/rsttest+tlrc. -b ${output_dir}/${output}+tlrc. -expr ‘ispositive(a)*b’ -prefix ${output_dir}/${output}_masked

echo “end”

If you have missing data, use 3dLME. The AFNI hands-on session for group analysis has a demo case (page 13):

https://afni.nimh.nih.gov/pub/dist/edu/data/CD.expanded/afni_handouts/afni25_GroupAna_HO.pdf