Gang,
Thank you for the feedback.
I'm having some issue trying to replicate the results from one voxel of a whole brain 3dLME analysis in SPSS and exclusively in R.
My model is a 2 factor repeated measures design with 1 within subject varying covariate.
If I try to run the below command in R
lme(values ~ time*treatment + ratings,data=lme_data,random = ~1 + ratings | subj)
I get the following error message:
nlminb problem, convergence error code = 1
message = iteration limit reached without convergence (10)
Here is the 3dLME equivalent? setup:
3dLME -prefix LME_Result' \
-model "time*treatment + ratings" \
-ranEff '~ 1 + ratings' \
-qvars 'ratings' \
-SS_type 3\
.
.
.
Is the R lme command line above the equivalent to the 3dLME model formula?
Just to simplify things, I tried to run lme without the covariate. Here is my model:
R_lme = lme(values ~ time*treatment ,data=lme_data, random = ~1 | subj)
3dLME equivalent setup:
3dLME -prefix LME_Result' \
-model "time*treatment " \
-ranEff '~ 1' \
-SS_type 3\
.
.
.
Is the R lme command line above the equivalent to the 3dLME model formula?
The results are different.
Running the LME in R: Here is my anova table from lme
anova.lme(R_lme)
numDF denDF F-value p-value
(Intercept) 1 112 0.000380997 0.9845
time 2 112 3.080942303 0.0498
treatment 2 112 10.352969615 0.0001
time:treatment 4 112 2.280583154 0.0650
3dLME result gives :
Intercept, 1 112 10.90502
Time main effect, df =2, 112 F = 2.357028, p = 0.0994
Treatment main effect, df = 2, 112 F = 8.43066, p = 0.00039
time*treatment interaction, df = 4, 112 F = 2.280609, p = 0.065
I get the same value for the time*treatment interaction, 2.281, but the treatment and time main effect F’s are different . Running the contrast in R using testInteraction between treatment1 vs treatment 2 yields the same results as 3dLME when not including the covariate. I am able to replicate the R lme results in SPSS too. Not sure what is going on. And why the main F's for 3dLME are different. What would account for the discrepancy in the results? Am I missing a small step in my analysis setup?
Here is the afni version we are using:
Precompiled binary linux_openmp_64: Feb 13 2015 (Version AFNI_2011_12_21_1014)
Michael.
Here is my model setup with the covariate included:
3dLME -prefix LME_Result' \
-model "time*treatment + ratings" \
-ranEff '~ 1 + ratings' \
-qvars 'ratings' \
-SS_type 3\
-num_glt 9 \
-gltLabel 1 treat1_vs_treat3 -gltCode 1 'treatment : 1*treat1 -1*treat3 ' \
-gltLabel 2 treat2_vs_treat3 -gltCode 2 'treatment : 1*treat2 -1*treat3 ' \
-gltLabel 3 treat1_vs_treat2 -gltCode 3 'treatment : 1*treat1 -1*treat2 ' \
-gltLabel 4 meanTime1 -gltCode 4 'time : 1*Time1 ' \
-gltLabel 5 meanTime2 -gltCode 5 'time : 1*Time2 ' \
-gltLabel 6 meanTime3 -gltCode 6 'time : 1*Time3 ' \
-gltLabel 7 meantreat1 -gltCode 7 'treatment : 1*treat1 ' \
-gltLabel 8 meantreat2 -gltCode 8 'treatment : 1*treat2 ' \
-gltLabel 9 meantreat3 -gltCode 9 'treatment : 1*treat3 ' \
-dataTable \
Subj time treatment ratings InputFile \
subj02 Time1 treat1 35.7037 Time1stats.subj02treat1file+tlrc \
subj02 Time1 treat2 -10.963 Time1stats.subj02treat2file+tlrc \
subj02 Time1 treat3 -4.2963 Time1stats.subj02treat3file+tlrc \
subj02 Time2 treat1 19.03704 Time2stats.subj02treat1file+tlrc \
subj02 Time2 treat2 -7.62963 Time2stats.subj02treat2file+tlrc \
subj02 Time2 treat3 -5.96296 Time2stats.subj02treat3file+tlrc \
subj02 Time3 treat1 19.03704 Time3stats.subj02treat1file+tlrc \
subj02 Time3 treat2 -9.2963 Time3stats.subj02treat2file+tlrc \
subj02 Time3 treat3 12.37037 Time3stats.subj02treat3file+tlrc \
subj09 Time1 treat1 -8.96296 Time1stats.subj09treat1file+tlrc \
subj09 Time1 treat2 7.037037 Time1stats.subj09treat2file+tlrc \
subj09 Time1 treat3 -7.62963 Time1stats.subj09treat3file+tlrc \
subj09 Time2 treat1 -10.963 Time2stats.subj09treat1file+tlrc \
subj09 Time2 treat2 -14.2963 Time2stats.subj09treat2file+tlrc \
subj09 Time2 treat3 -14.2963 Time2stats.subj09treat3file+tlrc \
subj09 Time3 treat1 25.7037 Time3stats.subj09treat1file+tlrc \
subj09 Time3 treat2 -14.2963 Time3stats.subj09treat2file+tlrc \
subj09 Time3 treat3 -7.62963 Time3stats.subj09treat3file+tlrc \
subj11 Time1 treat1 0.703704 Time1stats.subj11treat1file+tlrc \
subj11 Time1 treat2 22.37037 Time1stats.subj11treat2file+tlrc \
subj11 Time1 treat3 -2.62963 Time1stats.subj11treat3file+tlrc \
subj11 Time2 treat1 9.037037 Time2stats.subj11treat1file+tlrc \
subj11 Time2 treat2 -10.963 Time2stats.subj11treat2file+tlrc \
subj11 Time2 treat3 12.37037 Time2stats.subj11treat3file+tlrc \
subj11 Time3 treat1 -11.6296 Time3stats.subj11treat1file+tlrc \
subj11 Time3 treat2 0.703704 Time3stats.subj11treat2file+tlrc \
subj11 Time3 treat3 -5.96296 Time3stats.subj11treat3file+tlrc \
subj15 Time1 treat1 -11.6296 Time1stats.subj15treat1file+tlrc \
subj15 Time1 treat2 -14.2963 Time1stats.subj15treat2file+tlrc \
subj15 Time1 treat3 -14.2963 Time1stats.subj15treat3file+tlrc \
subj15 Time2 treat1 35.7037 Time2stats.subj15treat1file+tlrc \
subj15 Time2 treat2 2.37037 Time2stats.subj15treat2file+tlrc \
subj15 Time2 treat3 -4.2963 Time2stats.subj15treat3file+tlrc \
subj15 Time3 treat1 12.37037 Time3stats.subj15treat1file+tlrc \
subj15 Time3 treat2 5.703704 Time3stats.subj15treat2file+tlrc \
subj15 Time3 treat3 -7.62963 Time3stats.subj15treat3file+tlrc \
subj17 Time1 treat1 12.37037 Time1stats.subj17treat1file+tlrc \
subj17 Time1 treat2 -1.96296 Time1stats.subj17treat2file+tlrc \
subj17 Time1 treat3 5.703704 Time1stats.subj17treat3file+tlrc \
subj17 Time2 treat1 -13.6296 Time2stats.subj17treat1file+tlrc \
subj17 Time2 treat2 10.7037 Time2stats.subj17treat2file+tlrc \
subj17 Time2 treat3 -9.2963 Time2stats.subj17treat3file+tlrc \
subj17 Time3 treat1 -7.62963 Time3stats.subj17treat1file+tlrc \
subj17 Time3 treat2 -5.96296 Time3stats.subj17treat2file+tlrc \
subj17 Time3 treat3 -10.963 Time3stats.subj17treat3file+tlrc \
subj20 Time1 treat1 40.75556 Time1stats.subj20treat1file+tlrc \
subj20 Time1 treat2 5.755556 Time1stats.subj20treat2file+tlrc \
subj20 Time1 treat3 -10.9111 Time1stats.subj20treat3file+tlrc \
subj20 Time2 treat1 22.42222 Time2stats.subj20treat1file+tlrc \
subj20 Time2 treat2 -4.24444 Time2stats.subj20treat2file+tlrc \
subj20 Time2 treat3 -12.5778 Time2stats.subj20treat3file+tlrc \
subj20 Time3 treat1 9.088889 Time3stats.subj20treat1file+tlrc \
subj20 Time3 treat2 -6.91111 Time3stats.subj20treat2file+tlrc \
subj20 Time3 treat3 22.42222 Time3stats.subj20treat3file+tlrc \
subj25 Time1 treat1 -7.57778 Time1stats.subj25treat1file+tlrc \
subj25 Time1 treat2 14.08889 Time1stats.subj25treat2file+tlrc \
subj25 Time1 treat3 -15.9111 Time1stats.subj25treat3file+tlrc \
subj25 Time2 treat1 -9.24444 Time2stats.subj25treat1file+tlrc \
subj25 Time2 treat2 -17.5778 Time2stats.subj25treat2file+tlrc \
subj25 Time2 treat3 -17.2444 Time2stats.subj25treat3file+tlrc \
subj25 Time3 treat1 29.08889 Time3stats.subj25treat1file+tlrc \
subj25 Time3 treat2 -14.2444 Time3stats.subj25treat2file+tlrc \
subj25 Time3 treat3 -10.9111 Time3stats.subj25treat3file+tlrc \
subj29 Time1 treat1 5.755556 Time1stats.subj29treat1file+tlrc \
subj29 Time1 treat2 15.75556 Time1stats.subj29treat2file+tlrc \
subj29 Time1 treat3 -5.91111 Time1stats.subj29treat3file+tlrc \
subj29 Time2 treat1 9.088889 Time2stats.subj29treat1file+tlrc \
subj29 Time2 treat2 -9.24444 Time2stats.subj29treat2file+tlrc \
subj29 Time2 treat3 5.755556 Time2stats.subj29treat3file+tlrc \
subj29 Time3 treat1 -19.2444 Time3stats.subj29treat1file+tlrc \
subj29 Time3 treat2 9.088889 Time3stats.subj29treat2file+tlrc \
subj29 Time3 treat3 -9.24444 Time3stats.subj29treat3file+tlrc \
subj36 Time1 treat1 -12.5778 Time1stats.subj36treat1file+tlrc \
subj36 Time1 treat2 -20.9111 Time1stats.subj36treat2file+tlrc \
subj36 Time1 treat3 -18.5778 Time1stats.subj36treat3file+tlrc \
subj36 Time2 treat1 22.42222 Time2stats.subj36treat1file+tlrc \
subj36 Time2 treat2 22.42222 Time2stats.subj36treat2file+tlrc \
subj36 Time2 treat3 -4.24444 Time2stats.subj36treat3file+tlrc \
subj36 Time3 treat1 17.42222 Time3stats.subj36treat1file+tlrc \
subj36 Time3 treat2 25.75556 Time3stats.subj36treat2file+tlrc \
subj36 Time3 treat3 -10.9111 Time3stats.subj36treat3file+tlrc \
subj37 Time1 treat1 2.422222 Time1stats.subj37treat1file+tlrc \
subj37 Time1 treat2 -5.91111 Time1stats.subj37treat2file+tlrc \
subj37 Time1 treat3 9.088889 Time1stats.subj37treat3file+tlrc \
subj37 Time2 treat1 -13.2444 Time2stats.subj37treat1file+tlrc \
subj37 Time2 treat2 17.42222 Time2stats.subj37treat2file+tlrc \
subj37 Time2 treat3 -15.9111 Time2stats.subj37treat3file+tlrc \
subj37 Time3 treat1 -5.91111 Time3stats.subj37treat1file+tlrc \
subj37 Time3 treat2 -9.24444 Time3stats.subj37treat2file+tlrc \
subj37 Time3 treat3 -17.5778 Time3stats.subj37treat3file+tlrc \
subj38 Time1 treat1 29.92593 Time1stats.subj38treat1file+tlrc \
subj38 Time1 treat2 3.259259 Time1stats.subj38treat2file+tlrc \
subj38 Time1 treat3 -10.0741 Time1stats.subj38treat3file+tlrc \
subj38 Time2 treat1 34.92593 Time2stats.subj38treat1file+tlrc \
subj38 Time2 treat2 -6.74074 Time2stats.subj38treat2file+tlrc \
subj38 Time2 treat3 -10.0741 Time2stats.subj38treat3file+tlrc \
subj38 Time3 treat1 13.25926 Time3stats.subj38treat1file+tlrc \
subj38 Time3 treat2 -8.40741 Time3stats.subj38treat2file+tlrc \
subj38 Time3 treat3 6.592593 Time3stats.subj38treat3file+tlrc \
subj42 Time1 treat1 -15.0741 Time1stats.subj42treat1file+tlrc \
subj42 Time1 treat2 14.92593 Time1stats.subj42treat2file+tlrc \
subj42 Time1 treat3 -18.4074 Time1stats.subj42treat3file+tlrc \
subj42 Time2 treat1 -6.74074 Time2stats.subj42treat1file+tlrc \
subj42 Time2 treat2 -18.4074 Time2stats.subj42treat2file+tlrc \
subj42 Time2 treat3 -19.7407 Time2stats.subj42treat3file+tlrc \
subj42 Time3 treat1 33.25926 Time3stats.subj42treat1file+tlrc \
subj42 Time3 treat2 -6.74074 Time3stats.subj42treat2file+tlrc \
subj42 Time3 treat3 -13.4074 Time3stats.subj42treat3file+tlrc \
subj43 Time1 treat1 11.59259 Time1stats.subj43treat1file+tlrc \
subj43 Time1 treat2 29.92593 Time1stats.subj43treat2file+tlrc \
subj43 Time1 treat3 -8.40741 Time1stats.subj43treat3file+tlrc \
subj43 Time2 treat1 9.925926 Time2stats.subj43treat1file+tlrc \
subj43 Time2 treat2 -8.40741 Time2stats.subj43treat2file+tlrc \
subj43 Time2 treat3 13.25926 Time2stats.subj43treat3file+tlrc \
subj43 Time3 treat1 -18.0741 Time3stats.subj43treat1file+tlrc \
subj43 Time3 treat2 8.259259 Time3stats.subj43treat2file+tlrc \
subj43 Time3 treat3 -11.7407 Time3stats.subj43treat3file+tlrc \
subj44 Time1 treat1 -12.7407 Time1stats.subj44treat1file+tlrc \
subj44 Time1 treat2 -23.4074 Time1stats.subj44treat2file+tlrc \
subj44 Time1 treat3 -9.74074 Time1stats.subj44treat3file+tlrc \
subj44 Time2 treat1 26.59259 Time2stats.subj44treat1file+tlrc \
subj44 Time2 treat2 3.259259 Time2stats.subj44treat2file+tlrc \
subj44 Time2 treat3 -6.74074 Time2stats.subj44treat3file+tlrc \
subj44 Time3 treat1 28.25926 Time3stats.subj44treat1file+tlrc \
subj44 Time3 treat2 16.59259 Time3stats.subj44treat2file+tlrc \
subj44 Time3 treat3 -11.7407 Time3stats.subj44treat3file+tlrc \
subj47 Time1 treat1 6.592593 Time1stats.subj47treat1file+tlrc \
subj47 Time1 treat2 -6.74074 Time1stats.subj47treat2file+tlrc \
subj47 Time1 treat3 13.25926 Time1stats.subj47treat3file+tlrc \
subj47 Time2 treat1 -11.7407 Time2stats.subj47treat1file+tlrc \
subj47 Time2 treat2 11.59259 Time2stats.subj47treat2file+tlrc \
subj47 Time2 treat3 -16.7407 Time2stats.subj47treat3file+tlrc \
subj47 Time3 treat1 -13.4074 Time3stats.subj47treat1file+tlrc \
subj47 Time3 treat2 -8.40741 Time3stats.subj47treat2file+tlrc \
subj47 Time3 treat3 -13.4074 Time3stats.subj47treat3file+tlrc
