3dANOVA3

dawoon · April 28, 2017, 5:32pm

Dear AFNI experts,

I am looking for some advice to modeling the ANOVA (i.e. 3dANOVA3) in appropriate way.
(Before starting… I’m just a beginner in AFNI… so there could be many mistakes, issues, etc. on understanding of the function…)
In short, there are three factors in my data: factor1[fixed] - types (E, S) / factor2[fixed] - conditions (A, S) / factor3[random] - subjects (total 5; s01 ~ 05)

…	…factor1 types (E, S)
…factor2…	…EA (s01 ~ 05)…
conditions	----------------------------
…(A, S)…	…RA (s01 ~ 05)…

The things that I wanted to measure are, 1) main-effect of type, 2) main-effect of condition, and 3) interaction between type and condition.
Thus, I thought that I need to use 3dANOVA3, and the below is the one which I wrote to use.

3dANOVA3 -type 4
-alevels 2
-blevels 2
-clevels 5
-dset 1 1 1 EA_s01+tlrc \ -dset 1 2 1 ES_s01+tlrc
-dset 1 1 2 EA_s02+tlrc \ -dset 1 2 2 ES_s02+tlrc
-dset 1 1 3 EA_s03+tlrc \ -dset 1 2 3 ES_s03+tlrc
-dset 1 1 4 EA_s04+tlrc \ -dset 1 2 4 ES_s04+tlrc
-dset 1 1 5 EA_s05+tlrc \ -dset 1 2 5 ES_s05+tlrc
-dset 2 1 1 RA_s01+tlrc \ -dset 2 2 1 RS_s01+tlrc
-dset 2 1 2 RA_s02+tlrc \ -dset 2 2 2 RS_s02+tlrc
-dset 2 1 3 RA_s03+tlrc \ -dset 2 2 3 RS_s03+tlrc
-dset 2 1 4 RA_s04+tlrc \ -dset 2 2 4 RS_s04+tlrc
-dset 2 1 5 RA_s05+tlrc \ -dset 2 2 5 RS_s05+tlrc
-fa types
-fb conditions
-fab types_cond_interact
-adiff 1 2 EvsR
-bdiff 1 2 AvsS
-aBcontr 1 -1 : 1 EvsR_A
-aBcontr 1 -1 : 2 EvsR_S
-Abcontr 1 : 1 -1 AvsS_E
-Abcontr 2 : 1 -1 AvsS_R
-bucket donut_anova

However, I’m not sure, that it is correct to use.
Also, when I tried to find other methods, I could find ‘3dMEMA’, but still… I’m not sure which function is correct to use.

Thus, may I ask you,

whether the code is correct to use, relating to the point that I wanted to find.
whether it is correct function to use (is there any other options?).

Your advices will be appreciated.
Thank you.

Gang · April 28, 2017, 8:15pm

The 3dANOVA3 script looks fine to me. However, if you only have 5 subjects, you have power issue.

dawoon · May 3, 2017, 8:17am

Dear Gang,

Thank you for the comments.
Actually, there are 20 subjects in my data, and I tried to conduct the 3dANOVA3.
However, I had an issue in the “-bucket”, and below is the script which I used.

[Script]

set dirA = /path/to/anova/data

3dANOVA3 -type 4
-alevels 2
-blevels 2
-clevels 20
-dset 1 1 1 “$dirA/stats.s10_E_A_REML+tlrc[31]”
-dset 1 2 1 “$dirA/stats.s10_E_S_REML+tlrc[31]”
-dset 1 1 2 “$dirA/stats.s11_E_A_REML+tlrc[31]”
-dset 1 2 2 “$dirA/stats.s11_E_S_REML+tlrc[31]”
-dset 1 1 3 “$dirA/stats.s12_E_A_REML+tlrc[31]”
-dset 1 2 3 “$dirA/stats.s12_E_S_REML+tlrc[31]”
-dset 1 1 4 “$dirA/stats.s13_E_A_REML+tlrc[31]”
-dset 1 2 4 “$dirA/stats.s13_E_S_REML+tlrc[31]”
-dset 1 1 5 “$dirA/stats.s15_E_A_REML+tlrc[31]”
-dset 1 2 5 “$dirA/stats.s15_E_S_REML+tlrc[31]”
-dset 1 1 6 “$dirA/stats.s16_E_A_REML+tlrc[31]”
-dset 1 2 6 “$dirA/stats.s16_E_S_REML+tlrc[31]”
-dset 1 1 7 “$dirA/stats.s18_E_A_REML+tlrc[31]”
-dset 1 2 7 “$dirA/stats.s18_E_S_REML+tlrc[31]”
-dset 1 1 8 “$dirA/stats.s19_E_A_REML+tlrc[31]”
-dset 1 2 8 “$dirA/stats.s19_E_S_REML+tlrc[31]”
-dset 1 1 9 “$dirA/stats.s20_E_A_REML+tlrc[31]”
-dset 1 2 9 “$dirA/stats.s20_E_S_REML+tlrc[31]”
-dset 1 1 10 “$dirA/stats.s21_E_A_REML+tlrc[31]”
-dset 1 2 10 “$dirA/stats.s21_E_S_REML+tlrc[31]”
-dset 1 1 11 “$dirA/stats.s22_E_A_REML+tlrc[31]”
-dset 1 2 11 “$dirA/stats.s22_E_S_REML+tlrc[31]”
-dset 1 1 12 “$dirA/stats.s23_E_A_REML+tlrc[31]”
-dset 1 2 12 “$dirA/stats.s23_E_S_REML+tlrc[31]”
-dset 1 1 13 “$dirA/stats.s24_E_A_REML+tlrc[31]”
-dset 1 2 13 “$dirA/stats.s24_E_S_REML+tlrc[31]”
-dset 1 1 14 “$dirA/stats.s25_E_A_REML+tlrc[31]”
-dset 1 2 14 “$dirA/stats.s25_E_S_REML+tlrc[31]”
-dset 1 1 15 “$dirA/stats.s26_E_A_REML+tlrc[31]”
-dset 1 2 15 “$dirA/stats.s26_E_S_REML+tlrc[31]”
-dset 1 1 16 “$dirA/stats.s27_E_A_REML+tlrc[31]”
-dset 1 2 16 “$dirA/stats.s27_E_S_REML+tlrc[31]”
-dset 1 1 17 “$dirA/stats.s28_E_A_REML+tlrc[31]”
-dset 1 2 17 “$dirA/stats.s28_E_S_REML+tlrc[31]”
-dset 1 1 18 “$dirA/stats.s29_E_A_REML+tlrc[31]”
-dset 1 2 18 “$dirA/stats.s29_E_S_REML+tlrc[31]”
-dset 1 1 19 “$dirA/stats.s30_E_A_REML+tlrc[31]”
-dset 1 2 19 “$dirA/stats.s30_E_S_REML+tlrc[31]”
-dset 1 1 20 “$dirA/stats.s31_E_A_REML+tlrc[31]”
-dset 1 2 20 “$dirA/stats.s31_E_S_REML+tlrc[31]”
-dset 2 1 1 “$dirA/stats.s10_E_A_REML+tlrc[31]”
-dset 2 2 1 “$dirA/stats.s10_E_S_REML+tlrc[31]”
-dset 2 1 2 “$dirA/stats.s11_E_A_REML+tlrc[31]”
-dset 2 2 2 “$dirA/stats.s11_E_S_REML+tlrc[31]”
-dset 2 1 3 “$dirA/stats.s12_E_A_REML+tlrc[31]”
-dset 2 2 3 “$dirA/stats.s12_E_S_REML+tlrc[31]”
-dset 2 1 4 “$dirA/stats.s13_E_A_REML+tlrc[31]”
-dset 2 2 4 “$dirA/stats.s13_E_S_REML+tlrc[31]”
-dset 2 1 5 “$dirA/stats.s15_E_A_REML+tlrc[31]”
-dset 2 2 5 “$dirA/stats.s15_E_S_REML+tlrc[31]”
-dset 2 1 6 “$dirA/stats.s16_E_A_REML+tlrc[31]”
-dset 2 2 6 “$dirA/stats.s16_E_S_REML+tlrc[31]”
-dset 2 1 7 “$dirA/stats.s18_E_A_REML+tlrc[31]”
-dset 2 2 7 “$dirA/stats.s18_E_S_REML+tlrc[31]”
-dset 2 1 8 “$dirA/stats.s19_E_A_REML+tlrc[31]”
-dset 2 2 8 “$dirA/stats.s19_E_S_REML+tlrc[31]”
-dset 2 1 9 “$dirA/stats.s20_E_A_REML+tlrc[31]”
-dset 2 2 9 “$dirA/stats.s20_E_S_REML+tlrc[31]”
-dset 2 1 10 “$dirA/stats.s21_E_A_REML+tlrc[31]”
-dset 2 2 10 “$dirA/stats.s21_E_S_REML+tlrc[31]”
-dset 2 1 11 “$dirA/stats.s22_E_A_REML+tlrc[31]”
-dset 2 2 11 “$dirA/stats.s22_E_S_REML+tlrc[31]”
-dset 2 1 12 “$dirA/stats.s23_E_A_REML+tlrc[31]”
-dset 2 2 12 “$dirA/stats.s23_E_S_REML+tlrc[31]”
-dset 2 1 13 “$dirA/stats.s24_E_A_REML+tlrc[31]”
-dset 2 2 13 “$dirA/stats.s24_E_S_REML+tlrc[31]”
-dset 2 1 14 “$dirA/stats.s25_E_A_REML+tlrc[31]”
-dset 2 2 14 “$dirA/stats.s25_E_S_REML+tlrc[31]”
-dset 2 1 15 “$dirA/stats.s26_E_A_REML+tlrc[31]”
-dset 2 2 15 “$dirA/stats.s26_E_S_REML+tlrc[31]”
-dset 2 1 16 “$dirA/stats.s27_E_A_REML+tlrc[31]”
-dset 2 2 16 “$dirA/stats.s27_E_S_REML+tlrc[31]”
-dset 2 1 17 “$dirA/stats.s28_E_A_REML+tlrc[31]”
-dset 2 2 17 “$dirA/stats.s28_E_S_REML+tlrc[31]”
-dset 2 1 18 “$dirA/stats.s29_E_A_REML+tlrc[31]”
-dset 2 2 18 “$dirA/stats.s29_E_S_REML+tlrc[31]”
-dset 2 1 19 “$dirA/stats.s30_E_A_REML+tlrc[31]”
-dset 2 2 19 “$dirA/stats.s30_E_S_REML+tlrc[31]”
-dset 2 1 20 “$dirA/stats.s31_E_A_REML+tlrc[31]”
-dset 2 2 20 “$dirA/stats.s31_E_S_REML+tlrc[31]”
-fa types
-fb conditions
-fab types_cond_interact
-adiff 1 2 E_vs_R
-bdiff 1 2 A_vs_S
-aBcontr 1 -1 : 1 E_vs_R_A
-aBcontr 1 -1 : 2 E_vs_R_S
-Abcontr 1 : 1 -1 A_vs_S_E
-Abcontr 2 : 1 -1 A_vs_S_R
-bucket anova \

[Issue]
-bucket: Command not found
was appeared. I tried to find what is the problem, but I couldn’t get the solution…

Therefore… may I ask you what’s the problem in this part?
Thank you in advance.

rickr · May 3, 2017, 3:22pm

You are missing a line continuation character
at the end of the prior line. So the shell thinks
“-bucket” is supposed to be the start of a new
command (and 3dANOVA3 does not see that
option).

rick

dawoon · May 3, 2017, 3:50pm

Dear Rick,

Thank you for the comment!
Even I checked the script more than three times, I didn’t realize that I missed the '' at the end of the prior line…

Thanks!
DaWoon