3dLMEr hung or stuck on loading required package: snow

AFNI Message Board
1

Hi Gang,

3dLMEr was stuck (hung) at the step of loading required package: snow for a day. I have already installed the package “snow”, but I don’t see R is cranking because no memory was chewing up at the background.

See attached for the script.

Here is the message:

Loading required package: lmerTest
Loading required package: lme4
Loading required package: Matrix

Attaching package: ‘lmerTest’

The following object is masked from ‘package:lme4’:

lmer

The following object is masked from ‘package:stats’:

step

Loading required package: phia
Loading required package: car
Loading required package: carData
Registered S3 methods overwritten by ‘car’:
method from
influence.merMod lme4
cooks.distance.influence.merMod lme4
dfbeta.influence.merMod lme4
dfbetas.influence.merMod lme4
Loading required package: snow

Thank you.

Ping

Screen Shot 2020-09-25 at 3.05.17 PM.png
Screen Shot 2020-09-25 at 3.05.17 PM.png1349×787 220 KB

2

Ping,

Do you mean that it is stuck at the following line?

Loading required package: snow

If so, kill the process and then re-start the script. If the problem persists, that would be strange.

3

Hi Gang,

I re-run the script but it seems that it still stuck at the step of “Loading required package: snow”.

What syntax can I use to output the log?

Thank you.

Ping

4

Hi Gang,

It ran fine and output the results along with the FDR values. Sorry for the false alarm.

I have other questions regarding interpretating the contrasts. Here are the model and contrasts I used, there were 4 experimental groups and three time points, TP1, TP2, TP3

3dLMEr -prefix DTI_long
-jobs 6
-mask /Users/pyeh/bin/longDTI_npoint/mask.nii
-model ‘GroupTimePoint+Gender+Age+Daysinceinj+(1|ID)’
-qVars ‘Age,Daysinceinj’
-gltCode TP2-TP1controls-ComplicatedmTBI 'Group : 1control -1complicatedmTBI TimePoint : 1TP2 -1TP1’
-glfCode Baseline_maineffect_Control 'Group : 1control -1complicatedmTBI & 1control -1uncomplicatedmTBI & 1control -1modsevere TimePoint : 1TP1’ \

For the “Group : 1control -1complicatedmTBI TimePoint : 1TP2 -1TP1”, the z score means the control had larger slope (trajectory) than the complicatedmTBI group between TP2 and TP1?

,and “Group : 1control -1complicatedmTBI & 1control -1uncomplicatedmTBI & 1control -1modsevere TimePoint : 1*TP1’” was the F value of the TP1 main effect of the control group?

Thanks.

Ping

5

Hi Ping,

For the “Group : 1control -1complicatedmTBI TimePoint : 1TP2 -1TP1”, the z score means the control
had larger slope (trajectory) than the complicatedmTBI group between TP2 and TP1?

It compares the control group’s TP2 - TP1 to the complicatedmTBI group’s TP2 - TP1. You may want to add a few contrasts to help you tease it apart:

-gltCode TP2-TP1-controls ‘Group : 1control TimePoint : 1TP2 -1TP1’
-gltCode TP2-TP1-ComplicatedmTBI 'Group : 1complicatedmTBI TimePoint : 1TP2 -1TP1’
-gltCode TP1controls-ComplicatedmTBI ‘Group : 1control -1complicatedmTBI TimePoint : 1TP1’
-gltCode TP2controls-ComplicatedmTBI 'Group : 1control -1complicatedmTBI TimePoint : 1TP2’ \

“Group : 1control -1complicatedmTBI & 1control -1uncomplicatedmTBI & 1control -1modsevere TimePoint : 1*TP1’”
was the F value of the TP1 main effect of the control group?

Yes, it gives you the statistical evidence for the differences across the four groups at time point TP1.