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GroupAna_cases/1.3conds/run* : vert align opts #2

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698f402
GroupAna_cases/1.3conds/run* : vert align opts
mrneont May 30, 2025
f229c38
GroupAna_cases/2.3groups/run* : vert align opts
mrneont May 30, 2025
93edef6
GroupAna_cases/3.anova/run*: remove tabs and vert align opts
mrneont May 30, 2025
49df495
GroupAna_cases/4.lme/run*: remove tabs and vert align opts
mrneont May 30, 2025
70d3ac4
GroupAna_cases/5.mss/* : vert align opts and no tabs
mrneont May 30, 2025
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121 changes: 64 additions & 57 deletions AFNI_data6/GroupAna_cases/1.3conds/run.LME2.txt
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Expand Up @@ -20,60 +20,67 @@
# S122 1 1 1
# S123 1 1 1

3dLME -prefix result.LME2 -jobs 2 \
-model "Cond" \
-SS_type 3 \
-ranEff '~1' \
-num_glt 5 \
-gltLabel 1 'Ket' -gltCode 1 'Cond : 1*Ket' \
-gltLabel 2 'Ket-Placebo' -gltCode 2 'Cond : 1*Ket -1*Placebo' \
-gltLabel 3 'Ket-Placebo-Baseline' -gltCode 3 'Cond : 1*Ket -1*Placebo -1*Baseline' \
-gltLabel 4 'Ket-Baseline' -gltCode 4 'Cond : 1*Ket -1*Baseline' \
-gltLabel 5 'Ket-Placebo+Baseline2' -gltCode 5 'Cond : 1*Ket -1*Placebo +1*Baseline' \
-dataTable \
Subj Cond InputFile \
S101 Ket Ket/Subject101+tlrc \
S102 Ket Ket/Subject102+tlrc \
S105 Ket Ket/Subject105+tlrc \
S107 Ket Ket/Subject107+tlrc \
S108 Ket Ket/Subject108+tlrc \
S109 Ket Ket/Subject109+tlrc \
S110 Ket Ket/Subject110+tlrc \
S111 Ket Ket/Subject111+tlrc \
S112 Ket Ket/Subject112+tlrc \
S113 Ket Ket/Subject113+tlrc \
S115 Ket Ket/Subject115+tlrc \
S116 Ket Ket/Subject116+tlrc \
S118 Ket Ket/Subject118+tlrc \
S120 Ket Ket/Subject120+tlrc \
S121 Ket Ket/Subject121+tlrc \
S122 Ket Ket/Subject122+tlrc \
S123 Ket Ket/Subject123+tlrc \
S102 Placebo Placebo/Subject102+tlrc \
S105 Placebo Placebo/Subject105+tlrc \
S107 Placebo Placebo/Subject107+tlrc \
S108 Placebo Placebo/Subject108+tlrc \
S109 Placebo Placebo/Subject109+tlrc \
S110 Placebo Placebo/Subject110+tlrc \
S112 Placebo Placebo/Subject112+tlrc \
S113 Placebo Placebo/Subject113+tlrc \
S115 Placebo Placebo/Subject115+tlrc \
S118 Placebo Placebo/Subject118+tlrc \
S120 Placebo Placebo/Subject120+tlrc \
S122 Placebo Placebo/Subject122+tlrc \
S123 Placebo Placebo/Subject123+tlrc \
S101 Baseline Baseline/Subject101+tlrc \
S102 Baseline Baseline/Subject102+tlrc \
S105 Baseline Baseline/Subject105+tlrc \
S107 Baseline Baseline/Subject107+tlrc \
S108 Baseline Baseline/Subject108+tlrc \
S109 Baseline Baseline/Subject109+tlrc \
S110 Baseline Baseline/Subject110+tlrc \
S111 Baseline Baseline/Subject111+tlrc \
S113 Baseline Baseline/Subject113+tlrc \
S116 Baseline Baseline/Subject116+tlrc \
S118 Baseline Baseline/Subject118+tlrc \
S120 Baseline Baseline/Subject120+tlrc \
S121 Baseline Baseline/Subject121+tlrc \
S122 Baseline Baseline/Subject122+tlrc \
S123 Baseline Baseline/Subject123+tlrc
3dLME \
-prefix result.LME2 \
-jobs 2 \
-model "Cond" \
-SS_type 3 \
-ranEff '~1' \
-num_glt 5 \
-gltLabel 1 'Ket' \
-gltCode 1 'Cond : 1*Ket' \
-gltLabel 2 'Ket-Placebo' \
-gltCode 2 'Cond : 1*Ket -1*Placebo' \
-gltLabel 3 'Ket-Placebo-Baseline' \
-gltCode 3 'Cond : 1*Ket -1*Placebo -1*Baseline' \
-gltLabel 4 'Ket-Baseline' \
-gltCode 4 'Cond : 1*Ket -1*Baseline' \
-gltLabel 5 'Ket-Placebo+Baseline2' \
-gltCode 5 'Cond : 1*Ket -1*Placebo +1*Baseline' \
-dataTable \
Subj Cond InputFile \
S101 Ket Ket/Subject101+tlrc \
S102 Ket Ket/Subject102+tlrc \
S105 Ket Ket/Subject105+tlrc \
S107 Ket Ket/Subject107+tlrc \
S108 Ket Ket/Subject108+tlrc \
S109 Ket Ket/Subject109+tlrc \
S110 Ket Ket/Subject110+tlrc \
S111 Ket Ket/Subject111+tlrc \
S112 Ket Ket/Subject112+tlrc \
S113 Ket Ket/Subject113+tlrc \
S115 Ket Ket/Subject115+tlrc \
S116 Ket Ket/Subject116+tlrc \
S118 Ket Ket/Subject118+tlrc \
S120 Ket Ket/Subject120+tlrc \
S121 Ket Ket/Subject121+tlrc \
S122 Ket Ket/Subject122+tlrc \
S123 Ket Ket/Subject123+tlrc \
S102 Placebo Placebo/Subject102+tlrc \
S105 Placebo Placebo/Subject105+tlrc \
S107 Placebo Placebo/Subject107+tlrc \
S108 Placebo Placebo/Subject108+tlrc \
S109 Placebo Placebo/Subject109+tlrc \
S110 Placebo Placebo/Subject110+tlrc \
S112 Placebo Placebo/Subject112+tlrc \
S113 Placebo Placebo/Subject113+tlrc \
S115 Placebo Placebo/Subject115+tlrc \
S118 Placebo Placebo/Subject118+tlrc \
S120 Placebo Placebo/Subject120+tlrc \
S122 Placebo Placebo/Subject122+tlrc \
S123 Placebo Placebo/Subject123+tlrc \
S101 Baseline Baseline/Subject101+tlrc \
S102 Baseline Baseline/Subject102+tlrc \
S105 Baseline Baseline/Subject105+tlrc \
S107 Baseline Baseline/Subject107+tlrc \
S108 Baseline Baseline/Subject108+tlrc \
S109 Baseline Baseline/Subject109+tlrc \
S110 Baseline Baseline/Subject110+tlrc \
S111 Baseline Baseline/Subject111+tlrc \
S113 Baseline Baseline/Subject113+tlrc \
S116 Baseline Baseline/Subject116+tlrc \
S118 Baseline Baseline/Subject118+tlrc \
S120 Baseline Baseline/Subject120+tlrc \
S121 Baseline Baseline/Subject121+tlrc \
S122 Baseline Baseline/Subject122+tlrc \
S123 Baseline Baseline/Subject123+tlrc
32 changes: 19 additions & 13 deletions AFNI_data6/GroupAna_cases/1.3conds/run.LME2_table.txt
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@@ -1,4 +1,4 @@
# The data table is stored in a text file tbl.txt!!!
# ** The data table is stored in a text file tbl.txt **
# 1 group with 17 subjects
# 3 conditions: Baseline, Ket, Placebo
# Mising data with some subject
Expand All @@ -21,15 +21,21 @@
# S122 1 1 1
# S123 1 1 1

3dLME -prefix result.LME2_table -jobs 2 \
-model "Cond" \
-SS_type 3 \
-ranEff '~1' \
-num_glt 5 \
-gltLabel 1 'Ket' -gltCode 1 'Cond : 1*Ket' \
-gltLabel 2 'Ket-Placebo' -gltCode 2 'Cond : 1*Ket -1*Placebo' \
-gltLabel 3 'Ket-Placebo-Baseline' -gltCode 3 'Cond : 1*Ket -1*Placebo -1*Baseline' \
-gltLabel 4 'Ket-Baseline' -gltCode 4 'Cond : 1*Ket -1*Baseline' \
-gltLabel 5 'Ket-Placebo+Baseline2' -gltCode 5 'Cond : 1*Ket -1*Placebo +1*Baseline' \
-dataTable \
@tbl.txt
3dLME \
-prefix result.LME2_table \
-jobs 2 \
-model "Cond" \
-SS_type 3 \
-ranEff '~1' \
-num_glt 5 \
-gltLabel 1 'Ket' \
-gltCode 1 'Cond : 1*Ket' \
-gltLabel 2 'Ket-Placebo' \
-gltCode 2 'Cond : 1*Ket -1*Placebo' \
-gltLabel 3 'Ket-Placebo-Baseline' \
-gltCode 3 'Cond : 1*Ket -1*Placebo -1*Baseline' \
-gltLabel 4 'Ket-Baseline' \
-gltCode 4 'Cond : 1*Ket -1*Baseline' \
-gltLabel 5 'Ket-Placebo+Baseline2' \
-gltCode 5 'Cond : 1*Ket -1*Placebo +1*Baseline' \
-dataTable @tbl.txt
81 changes: 41 additions & 40 deletions AFNI_data6/GroupAna_cases/2.3groups/run.1_ANOVA.txt
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Expand Up @@ -2,44 +2,45 @@
# Unequal number of subjects across groups
# 1 effect estimate per subject

3dANOVA -levels 3 \
-ftr omnibusF \
-mean 1 VV \
-mean 2 VM \
-mean 3 MM \
-diff 1 2 VVvsVM \
-diff 2 3 VMvsMM \
-diff 1 3 VVvsMM \
-bucket result.1_ANOVA \
-dset 1 data/as+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/cg+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/cm+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/db+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/dh+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/dt+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/gm+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/hb+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/js+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/kb+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/mg+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/ph+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/pl+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/ro+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/te+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/tf+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/zy+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/ee+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/jl+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/jp+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/kc+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/rb+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 3 data/aw+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 3 data/fc+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 3 data/jd+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 3 data/jh+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 3 data/nb+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 3 data/ps+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 3 data/sh+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 3 data/sk+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 3 data/yj+tlrc'[HO_resvnr_mvn#0_Coef]'
3dANOVA \
-levels 3 \
-ftr omnibusF \
-mean 1 VV \
-mean 2 VM \
-mean 3 MM \
-diff 1 2 VVvsVM \
-diff 2 3 VMvsMM \
-diff 1 3 VVvsMM \
-bucket result.1_ANOVA \
-dset 1 data/as+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/cg+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/cm+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/db+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/dh+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/dt+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/gm+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/hb+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/js+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/kb+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/mg+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 1 data/ph+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/pl+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/ro+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/te+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/tf+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/zy+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/ee+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/jl+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/jp+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/kc+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 2 data/rb+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 3 data/aw+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 3 data/fc+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 3 data/jd+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 3 data/jh+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 3 data/nb+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 3 data/ps+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 3 data/sh+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 3 data/sk+tlrc'[HO_resvnr_mvn#0_Coef]' \
-dset 3 data/yj+tlrc'[HO_resvnr_mvn#0_Coef]'

54 changes: 28 additions & 26 deletions AFNI_data6/GroupAna_cases/2.3groups/run.2_ttest_2grps.txt
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Expand Up @@ -4,30 +4,32 @@
# By default 3dttest++ can only compare two groups
# Group comparison: A-B

3dttest++ -prefix result.2_ttest_2grps \
-covariates cov_2grps.1D -center DIFF \
-setA VV \
as data/as+tlrc'[HO_resvnr_mvn#0_Coef]' \
cg data/cg+tlrc'[HO_resvnr_mvn#0_Coef]' \
cm data/cm+tlrc'[HO_resvnr_mvn#0_Coef]' \
db data/db+tlrc'[HO_resvnr_mvn#0_Coef]' \
dh data/dh+tlrc'[HO_resvnr_mvn#0_Coef]' \
dt data/dt+tlrc'[HO_resvnr_mvn#0_Coef]' \
gm data/gm+tlrc'[HO_resvnr_mvn#0_Coef]' \
hb data/hb+tlrc'[HO_resvnr_mvn#0_Coef]' \
js data/js+tlrc'[HO_resvnr_mvn#0_Coef]' \
kb data/kb+tlrc'[HO_resvnr_mvn#0_Coef]' \
mg data/mg+tlrc'[HO_resvnr_mvn#0_Coef]' \
ph data/ph+tlrc'[HO_resvnr_mvn#0_Coef]' \
-setB VM \
pl data/pl+tlrc'[HO_resvnr_mvn#0_Coef]' \
ro data/ro+tlrc'[HO_resvnr_mvn#0_Coef]' \
te data/te+tlrc'[HO_resvnr_mvn#0_Coef]' \
tf data/tf+tlrc'[HO_resvnr_mvn#0_Coef]' \
zy data/zy+tlrc'[HO_resvnr_mvn#0_Coef]' \
ee data/ee+tlrc'[HO_resvnr_mvn#0_Coef]' \
jl data/jl+tlrc'[HO_resvnr_mvn#0_Coef]' \
jp data/jp+tlrc'[HO_resvnr_mvn#0_Coef]' \
kc data/kc+tlrc'[HO_resvnr_mvn#0_Coef]' \
rb data/rb+tlrc'[HO_resvnr_mvn#0_Coef]'
3dttest++ \
-prefix result.2_ttest_2grps \
-covariates cov_2grps.1D \
-center DIFF \
-setA VV \
as data/as+tlrc'[HO_resvnr_mvn#0_Coef]' \
cg data/cg+tlrc'[HO_resvnr_mvn#0_Coef]' \
cm data/cm+tlrc'[HO_resvnr_mvn#0_Coef]' \
db data/db+tlrc'[HO_resvnr_mvn#0_Coef]' \
dh data/dh+tlrc'[HO_resvnr_mvn#0_Coef]' \
dt data/dt+tlrc'[HO_resvnr_mvn#0_Coef]' \
gm data/gm+tlrc'[HO_resvnr_mvn#0_Coef]' \
hb data/hb+tlrc'[HO_resvnr_mvn#0_Coef]' \
js data/js+tlrc'[HO_resvnr_mvn#0_Coef]' \
kb data/kb+tlrc'[HO_resvnr_mvn#0_Coef]' \
mg data/mg+tlrc'[HO_resvnr_mvn#0_Coef]' \
ph data/ph+tlrc'[HO_resvnr_mvn#0_Coef]' \
-setB VM \
pl data/pl+tlrc'[HO_resvnr_mvn#0_Coef]' \
ro data/ro+tlrc'[HO_resvnr_mvn#0_Coef]' \
te data/te+tlrc'[HO_resvnr_mvn#0_Coef]' \
tf data/tf+tlrc'[HO_resvnr_mvn#0_Coef]' \
zy data/zy+tlrc'[HO_resvnr_mvn#0_Coef]' \
ee data/ee+tlrc'[HO_resvnr_mvn#0_Coef]' \
jl data/jl+tlrc'[HO_resvnr_mvn#0_Coef]' \
jp data/jp+tlrc'[HO_resvnr_mvn#0_Coef]' \
kc data/kc+tlrc'[HO_resvnr_mvn#0_Coef]' \
rb data/rb+tlrc'[HO_resvnr_mvn#0_Coef]'

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