3dANOVA3 for a 3-way, within-subject?

AbrahamSV · December 17, 2023, 3:15pm

AFNI version info (afni -ver): 23.3.13

Hi! I was wondering... Would it be correct to estimate a 3-way within-subject ANOVA?
Say I have 30 subjects that go through the same 3 conditions, 2 levels each (2x2x2). Something like all participants viewing objects that are:

abstract-small-colored (1-1-1)
abstract-small-grey (1-1-2)
abstract-big-colored (1-2-1)
abstract-big-grey (1-2-2)
concrete-small-colored (2-1-1)
concrete-small-grey (2-1-2)
concrete-big-colored (2-2-1)
concrete-big-grey (2-2-2)

Although this is a made-up example, I know that conceptually, it would make sense to test these 3 factors and their interactions, but is it statistically sound to run this type of ANOVA using 3dANOVA3? (Instead of running 2-3 versions with the collapsed conditions). All examples I see are max. 2-way + a between-subject factor.

Of course I can run:

3dANOVA3 -type 1                                                                     \
    -alevels 2                                                                       \
    -blevels 2                                                                       \
    -clevels 2                                                                       \
    -dset  1  1  1 "sub-00.results/rall_func+tlrc.HEAD[cond_1-1-1#0_Coef]" \
    -dset  1  1  2 "sub-00.results/rall_func+tlrc.HEAD[cond_1-1-2#0_Coef]"  \
    -dset  1  2  1 "sub-00.results/rall_func+tlrc.HEAD[cond_1-2-1#0_Coef]" \
 ...
    -dset  2  1  2 "sub-29.results/rall_func+tlrc.HEAD[cond_2-1-2#0_Coef]"  \
    -dset  2  2  2 "sub-29.results/rall_func+tlrc.HEAD[cond_2-2-2#0_Coef]" \
 ...
[contrasts and options]

...but I'm not sure if 3dANOVA3 is meant to run this. Also, gen_group_command.py is not meant to generate this kind of analyses. If it is sound, it would be good to have the option to avoid the tedious scripting.

Thanks in advance!

Gang · December 18, 2023, 3:40am

The 3dANOVA3 -type 4 program is suitable for conducting a two-way within-subject ANOVA but does not support three-way within-subject ANOVA. If you need to analyze a 2 \times 2 \times 2 within-subject ANOVA, you can utilize either 3dMVM or 3dLMEr . For guidance on model specification with 3dLMEr , refer to this blog post.

Gang Chen

AbrahamSV · December 21, 2023, 10:04am

Dear Gang Chen,

Thank you for your advice.

I've been delving into 3dLMEr and 3dMVM, and decided to go with 3dLMEr because this way I can run the 2x2x2 while controlling for a quantitative variable (RT).

Here is what I've been trying after checking the post you shared:

3dLMEr -prefix group_results/lme/lme_res -jobs 12                                                                                                                   \
 -model 'concr*fam*freq*RT+(1+RT|Subj)+(1+RT|concr:Subj)+(1+RT|fam:Subj)+(1+RT|freq:Subj)+(1+RT|concr:fam:Subj)+(1+RT|concr:freq:Subj)+(1+RT|fam:freq:Subj)'        \
 -SS_type 3                                                                                                                                                         \
 -glfCode abs_famxfreq 'concr : 1*abs fam : 1*lfam -1*hfam freq : 1*low -1*hi'                                                                                      \
 -glfCode con_famxfreq 'concr : 1*con fam : 1*lfam -1*hfam freq : 1*low -1*hi'                                                                                      \
 -gltCode abs-con 'concr : 1*abs -1*con fam : 1*lfam & 1*hfam freq : 1*low & 1*hi'                                                                                  \
 -gltCode lfam-hfam 'concr : 1*abs & 1*con fam : 1*lfam -1*hfam freq : 1*low & 1*hi'                                                                                \
 -gltCode low-hi 'concr : 1*abs & 1*con fam : 1*lfam & 1*hfam freq : 1*low -1*hi'                                                                                   \
 -data_table @anova_table.txt

However, I have a couple of doubts/issues:

Is this a correct way to estimate what I wanted?
When I run this (or other different models) I keep getting the error:

** Error: 
   Expecting 1 parameters for option "-model".
   Have 3 parameter(s) in string "concr*fam*freq*RT+(1+RT|Subj)+(1+RT|concr:Subj)+(1+RT|fam:Subj)+(1+RT|freq:Subj)+(1+RT|concr:fam:Subj)+(1+RT|concr:freq:Subj)+(1+RT|fam:freq:Subj) -SS_type 3" instead.
   NOTE that -SS_type in bad option above is not a recognized option.

** Error: 
   Error parsing arguments. See 3dLMEr -help for details.

Also checked the quotes and tried all types of quotes, but made no difference.
I run it as a .sh script and also by copying in the terminal, but it makes no difference.
I checked the script with

file_tool -test -infile [script]

And it gave me no errors.

I'm a bit puzzled, and I'm sure I'm missing something reeaaally basic... Any idea?

Thank you!!

Gang · December 21, 2023, 3:58pm

Is this a correct way to estimate what I wanted?

Including RT as a covariate can be tricky. I suggest the following:

It might be necessary to center RT within each of 8 combinations. Check the discussion here.
It would be prudent to run the analysis without RT and compare the results.

When I run this (or other different models) I keep getting the error

What is your AFNI version (afni -ver)? Update your AFNI and try the script again.

>  -glfCode abs_famxfreq 'concr : 1*abs fam : 1*lfam -1*hfam freq : 1*low -1*hi'                                                                                      \
>  -glfCode con_famxfreq 'concr : 1*con fam : 1*lfam -1*hfam freq : 1*low -1*hi'                                                                                      \

These two tests have one degree of freedom, so it would be more straightforward to use -gltCode (instead of -glfCode) to obtain the sign of the comparisons.

  -gltCode abs-con 'concr : 1*abs -1*con fam : 1*lfam & 1*hfam freq : 1*low & 1*hi'                                                                                  \
-gltCode lfam-hfam 'concr : 1*abs & 1*con fam : 1*lfam -1*hfam freq : 1*low & 1*hi'                                                                                \
-gltCode low-hi 'concr : 1*abs & 1*con fam : 1*lfam & 1*hfam freq : 1*low -1*hi'                                                                                   \

These three lines lack clarity and 3dLMEr would not accept them. Could you provide more details regarding your intended comparisons?

Gang Chen

AbrahamSV · December 22, 2023, 9:40am

Thank you for your reply.

Ok perfect. I will do as you say for the RT.

What is your AFNI version (afni -ver)? Update your AFNI and try the script again.

I was indeed running with an older version of AFNI, and some R packages where giving problems. After updating it the error disappeared.

These two tests have one degree of freedom, so it would be more straightforward to use -gltCode (instead of -glfCode) to obtain the sign of the comparisons.

  -glfCode abs_famxfreq 'concr : 1*abs fam : 1*lfam -1*hfam freq : 1*low -1*hi'                                                                                      \
-glfCode con_famxfreq 'concr : 1*con fam : 1*lfam -1*hfam freq : 1*low -1*hi'                                                                                      \

My intention was to check main effects and interaction of B (fam) and C (freq), while fixing A(concr) at each of the 2 levels. How would that be expressed? I think I misread the 3dLMEr -help then?

These three lines lack clarity and 3dLMEr would not accept them. Could you provide more details regarding your intended comparisons?

-gltCode abs-con 'concr : 1*abs -1*con fam : 1*lfam & 1*hfam freq : 1*low & 1*hi'                                                                                  \
-gltCode lfam-hfam 'concr : 1*abs & 1*con fam : 1*lfam -1*hfam freq : 1*low & 1*hi'                                                                                \
-gltCode low-hi 'concr : 1*abs & 1*con fam : 1*lfam & 1*hfam freq : 1*low -1*hi'                                                                                   \

Here I just wanted to check simple effects in A, B and C separately. This is, level 1 of A vs level 2 of A, collapsing the levels of B and C. Same for the other factors.

I found a new issue though... It seems my dataTable is not rectangular:

Error in if (len%%wd != 0) errex.AFNI(paste("The content under -dataTable is not rectangular!",  : 
  argument is of length zero

I checked and there are no bad characters, no spaces after backslash or whatsoever. I tried both by providing the file with @dataTable, and by copying it directly on the script, but I get the same. I also tried adding/removing the quotes for the brackets. The table looks like this:

Subj	RT	concr	fam	freq	InputFile	\
sub-00	0.8306	abs	lfam	low	sub-00.results/regress/rall_func+tlrc[abs_lfam_low#0_Coef]	\
sub-00	0.7518	abs	lfam	hi	sub-00.results/regress/rall_func+tlrc[abs_lfam_hi#0_Coef]	\
sub-00	0.7674	abs	hfam	low	sub-00.results/regress/rall_func+tlrc[abs_hfam_low#0_Coef]	\
sub-00	0.6828	abs	hfam	hi	sub-00.results/regress/rall_func+tlrc[abs_hfam_hi#0_Coef]	\
sub-00	0.8367	con	lfam	low	sub-00.results/regress/rall_func+tlrc[con_lfam_low#0_Coef]	\
sub-00	0.7632	con	lfam	hi	sub-00.results/regress/rall_func+tlrc[con_lfam_hi#0_Coef]	\
sub-00	0.736	con	hfam	low	sub-00.results/regress/rall_func+tlrc[con_hfam_low#0_Coef]	\
sub-00	0.6861	con	hfam	hi	sub-00.results/regress/rall_func+tlrc[con_hfam_hi#0_Coef]	\

...

sub-29	0.7152	abs	lfam	low	sub-29.results/regress/rall_func+tlrc[abs_lfam_low#0_Coef]	\
sub-29	0.6164	abs	lfam	hi	sub-29.results/regress/rall_func+tlrc[abs_lfam_hi#0_Coef]	\
sub-29	0.6045	abs	hfam	low	sub-29.results/regress/rall_func+tlrc[abs_hfam_low#0_Coef]	\
sub-29	0.5931	abs	hfam	hi	sub-29.results/regress/rall_func+tlrc[abs_hfam_hi#0_Coef]	\
sub-29	0.662	con	lfam	low	sub-29.results/regress/rall_func+tlrc[con_lfam_low#0_Coef]	\
sub-29	0.6076	con	lfam	hi	sub-29.results/regress/rall_func+tlrc[con_lfam_hi#0_Coef]	\
sub-29	0.6019	con	hfam	low	sub-29.results/regress/rall_func+tlrc[con_hfam_low#0_Coef]	\
sub-29	0.6088	con	hfam	hi	sub-29.results/regress/rall_func+tlrc[con_hfam_hi#0_Coef]

Gang · December 22, 2023, 12:46pm

-glfCode abs_famxfreq 'concr : 1*abs fam : 1*lfam -1*hfam freq : 1*low -1*hi'                                                                                      \
-glfCode con_famxfreq 'concr : 1*con fam : 1*lfam -1*hfam freq : 1*low -1*hi'                                                                                      \

My intention was to check main effects and interaction of B (fam) and C (freq), while fixing A(concr) at each of the 2 levels. How would that be expressed? I think I misread the 3dLMEr -help then?

For the main effects of B and C while fixing A(concr) at each of the 2 levels, add

-gltCode abs_fam 'concr : 1*abs fam : 1*lfam -1*hfam '                                                                                      \
-gltCode con_fam 'concr : 1*con fam : 1*lfam -1*hfam'                                                                                      \
-gltCode abs_freq 'concr : 1*abs freq : 1*low -1*hi'                                                                                      \
-gltCode con_freq 'concr : 1*con freq : 1*low -1*hi'                                                                                      \

For the interaction of B (fam) and C (freq) while fixing A(concr) at each of the 2 levels, add

-gltCode abs_famxfreq 'concr : 1*abs fam : 1*lfam -1*hfam freq : 1*low -1*hi'                                                                                      \
-gltCode con_famxfreq 'concr : 1*con fam : 1*lfam -1*hfam freq : 1*low -1*hi'                                                                                      \

Here I just wanted to check simple effects in A, B and C separately. This is, level 1 of A vs level 2 of A, collapsing the levels of B and C. Same for the other factors.

-gltCode abs-con 'concr : 1*abs -1*con fam : 1*lfam & 1*hfam freq : 1*low & 1*hi'                                                                                  \
-gltCode lfam-hfam 'concr : 1*abs & 1*con fam : 1*lfam -1*hfam freq : 1*low & 1*hi'                                                                                \
-gltCode low-hi 'concr : 1*abs & 1*con fam : 1*lfam & 1*hfam freq : 1*low -1*hi'                                                                                   \

Change your original specifications to:

-gltCode abs-con 'concr : 1*abs -1*con'   \
-gltCode lfam-hfam 'fam : 1*lfam -1*hfam' \
-gltCode low-hi 'freq : 1*low -1*hi'      \

It seems my dataTable is not rectangular

One possibility is that at least one line is missing one or more items (or having one or more extra items). @discoraj , could you provide some diagnosis help?

Gang Chen

AbrahamSV · December 22, 2023, 2:59pm

For extra info:
I have checked the table upside down. I see no missing/extra values.
I also tried different separators (the table I shared earlier was separated by \t), and different file formats.

Regarding the centering of RT, is it possible to provide the 8 centering values (e.g. the mean of each condition)? Like this:

-qVars RT
-qVarCenters '0.745,0.66,0.642,0.588,0.712,0.656,0.632,0.604'

Or should I just replace the RTs with their Z values in the dataTable?

Cheers!

Gang · December 22, 2023, 5:51pm

Regarding the centering of RT, is it possible to provide the 8 centering values (e.g. the mean of each condition)? ... Or should I just replace the RTs with their Z values in the dataTable?

3dLMEr currently lacks an inherent within-cell centering mechanism. To address this, you may need to manually center the RT values for each of the 8 combinations. This can be achieved using loops in a programming language. Then integrate the centered values back into the table.

It would be interesting to check the differences between with and without incorporating RT.

I have checked the table upside down. I see no missing/extra values.

If you share the script and table via email, I can take a close look.

Gang Chen

P. S.

Upon careful examination of the script, a subtle error has been identified. The line

-data_table @anova_table.txt

should be

-dataTable @anova_table.txt