3dMVM error message

AFNI Message Board
1

Dear AFNI expert,

After updating AFNI, I did 3dMVM with script like below (table.txt included paths for MNI spaced cope files)

3dMVM -prefix Emo_MVM -jobs 8 -bsVars 1 -wsVars "var01var02" -wsE2 -num_glt 12
-mask MNI152_T1_2mm_brain_mask.nii.gz
-gltLabel 1 c01_vs_c02 -gltCode 1 'var01 : 1c01 var02 : 1c02 -1c03’
…
-gltLabel 12 …
-dataTable @table.txt

Unfortunately, I faced on error messages.

  1. Error messages encountered like below:
    Welcome to afex. Important changes in the current version:
  • Functions for ANOVAs have been renamed to: aov_car(), aov_ez(), and aov_4().
  • ANOVA functions return an object of class ‘afex_aov’ as default, see: ?aov_car
  • ‘afex_aov’ objects can be passed to lsmeans for contrasts and follow-up tests.
  • Reset previous (faster) behavior via: afex_options(return_aov=‘nice’)
  • Many more arguments can now be set globally via options, see: afex_options()

load package: car
Loading required package: snow
Error in checkForRemoteErrors(val) :
2 nodes produced errors; first error: length is 0
Calls: aperm … clusterApply → staticClusterApply → checkForRemoteErrors
warning messages:
In summary.Anova.mlm(object$Anova, multivariate = FALSE) :
HF eps > 1 treated as 1

  1. after change from -jobs 8 to -jobs 1, the error message encountered like below:
    load package: car
    Error in if (p_wsmvt < uvfm$anova[ii, “Pr(>F)”]) out[ii] ← qf(p_wsmvt, :
    length is 0
    Calls: aperm → apply → FUN
    warning messages:
    In summary.Anova.mlm(object$Anova, multivariate = FALSE) :
    HF eps > 1 treated as 1

It will be great pleasure if know the solution for error messages.
Thank you,
Jeong

2

Jeong,

Try the following:

  1. make sure you have the most recent version of AFNI:

@update.afni.binaries -d

  1. have all the required R packages installed:

rPkgsInstall -pkgs ALL

  1. remove option "-wsE2 " from your 3dMVM script

  2. run the following command if you still have trouble running the script:

afni_system_check.py -check_all

3

Hi Gang,

It turns out the error messages derived from both -wsE2 option and wrong path for R package.
Thank you so much.

I have one question regarding output.
I expected I could get the same number of t-stats image as the no. of gltLabel (in my case, 12).
However, just one output file was produced after performing 3dMVM script.
Here is the output which was printed in terminal.

++ Smallest FDR q [0 (Intercept) F] = 6.99541e-07
++ Smallest FDR q [1 c01 F] = 7.63635e-08
++ Smallest FDR q [2 c02 F] = 4.77009e-13
++ Smallest FDR q [3 c01:c02 F] = 3.48735e-05
++ Smallest FDR q [5 … t] = 6.70835e-07
++ Smallest FDR q [7 … t] = 3.05506e-08
++ Smallest FDR q [9 … t] = 0.00627071
++ Smallest FDR q [11 vs t] = 1.56036e-08
++ Smallest FDR q [13 vs t] = 1.54795e-06
++ Smallest FDR q [15 vs t] = 8.3346e-06
++ Smallest FDR q [17 vs t] = 0.00029295
++ Smallest FDR q [19 vs t] = 1.13479e-06
++ Smallest FDR q [21 2way_interaction t] = 0.00208255
*+ WARNING: Smallest FDR q [23 2way_interaction t] = 0.832452 ==> few true single voxel detections
++ Smallest FDR q [25 2way_interaction t] = 0.00813095
++ Smallest FDR q [27 2way_interaction t] = 0.00293417
*+ WARNING: varying brick factors, writing NIfTI as float
In summary.Anova.mlm(object$Anova, multivariate = FALSE) :
HF eps > 1 treated as 1

Thank you for your great help.

Jeong

4

Jeong,

The part you saw on the terminal is not really the full output information, but something about the FDR calculations for those statistical sub-bricks. To see all the sub-bricks, try

3dinfo -verb your_output_file