Issue with 3dMVM

AFNI Message Board
1

Hello,

I am having trouble running 3dMVM and get the following error upon running the script I have created. Any help you could provide regarding overcoming this issue would be greatly appreciated.

updating R_LD_LIBRARY_PATH …

oo Warning:
Failed to load R_io.so with this error message:

Error in dyn.load(ll) :
unable to load shared object ‘/Users/jessedesimone/abin/R_io.so’:
dlopen(/Users/jessedesimone/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/jessedesimone/abin/R_io.so
Reason: image not found
Calls: source … withVisible → eval → eval → set_R_io → dyn.load
Execution halted

I just recently updated my afni binaries using:
@update.afni.binaries -package macos_10.12_local

afni -version
Precompiled binary macos_10.12_local: Jul 23 2020 (Version AFNI_20.2.06 ‘Aulus Vitellius’)

Version of R:

version
_
platform x86_64-apple-darwin17.0
arch x86_64
os darwin17.0
system x86_64, darwin17.0
status
major 4
minor 0.2
year 2020
month 06
day 22
svn rev 78730
language R
version.string R version 4.0.2 (2020-06-22)
nickname Taking Off Again

2

At the moment there is an issue with the R version 4.* for some AFNI programs that use R. A temporary solution is to install an older version of R, for example, 3.6.3:

https://cran.r-project.org/bin/macosx/R-3.6.3.nn.pkg

3

Thanks Gang.

Installing R version 3.6.3 appears to work. Looks like it is reading the data appropriately for MVM analysis. However, I am getting the following error:

Error in xinit : object ‘xinit’ not found
Execution halted

See summary below:

***** Summary information of data structure *****
9 subjects : Subj1 Subj2 Subj3 Subj4 Subj5 Subj6 Subj7 Subj8 Subj9
9 response values
3 levels for factor group : CT YTh YTl
9 centered values for numeric variable age : -1 0 1 -1 0 1 -1 0 1
9 centered values for numeric variable bmi : -1 0 1 -1 0 1 -1 0 1
3 post hoc tests

Contingency tables of subject distributions among the categorical variables:

group
CT YTh YTl
3 3 3

Tabulation of subjects against each of the categorical variables:

lop$nSubj vs group:
                      
                       CT YTh YTl
  Subj1    0   1   0
  Subj2    0   1   0
  Subj3    0   1   0
  Subj4    0   0   1
  Subj5    0   0   1
  Subj6    0   0   1
  Subj7  1   0   0
  Subj8  1   0   0
  Subj9  1   0   0

***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

Reading input files now...

Reading input files: Done!


Range of input data: [-1.250, 1.692]

If the program hangs here for more than, for example, half an hour,
kill the process because the model specification or the GLT coding
is likely inappropriate.

Error in xinit : object 'xinit' not found
Execution halted
4

The error message is not a little strange. You only have 3 subjects in each group? Plus, these are the centered values of the age and bmi?

9 centered values for numeric variable age : -1 0 1 -1 0 1 -1 0 1
9 centered values for numeric variable bmi : -1 0 1 -1 0 1 -1 0 1

5

HI Gang,

I was using 3 subjects in each group simply to test the Script. I have 3 groups all with more than 20 subjects. I have acquired a single resting scan for each subject and computed Z-score coverted pearson correlation maps from a single ROI for each subject (input files). The goal is to compare all 3 groups using all combinations (g1 vs g2, g2 vs g3, g1 vs g3) while covarying for age and bmi across subjects.

Here is an example of the script I created.

3dMVM -prefix MVMtest1 -jobs 1
-mask /Users/jessedesimone/Desktop/MVM_analysis/Templates/network_masks_thr005/DAN_12mm_ntwk+tlrc
-bsVars "groupage+bmi"
-qVars age,bmi
-num_glt 3
-gltLabel 1 g1_vs_g2 -gltCode 1 'group : 1g1 -1g2’
-gltLabel 2 g1_vs_g3 -gltCode 2 'group : 1g1 -1g3’
-gltLabel 3 g2_vs_g3 -gltCode 3 'group : 1g2 -1*g3’
-dataTable @/Users/jessedesimone/Desktop/MVM_analysis/flists/datatab.txt

Here is the input for datatab.txt. These are manufactured values for age and bmi - simply for testing purposes before input of the actual values.

Subj group age bmi InputFile
subj1 g1 11 20 subj1.DAN_12mm_RS+tlrc.HEAD[PearCorr#0]
subj2 g1 12 21 subj2.DAN_12mm_RS+tlrc.HEAD[PearCorr#0]
subj3 g1 13 22 subj3.DAN_12mm_RS+tlrc.HEAD[PearCorr#0]
subj4 g2 11 20 subj4.DAN_12mm_RS+tlrc.HEAD[PearCorr#0]
subj5 g2 12 21 subj5.DAN_12mm_RS+tlrc.HEAD[PearCorr#0]
subj6 g2 13 22 subj6.DAN_12mm_RS+tlrc.HEAD[PearCorr#0]
subj7 g3 11 20 subj7.DAN_12mm_RS+tlrc.HEAD[PearCorr#0]
subj8 g3 12 21 subj8.DAN_12mm_RS+tlrc.HEAD[PearCorr#0]
subj9 g3 13 22 subj9.DAN_12mm_RS+tlrc.HEAD[PearCorr#0]

6

the script seems like it is reading the data correctly. Is the xinit error related to R