Hi Gang,
I know this is an old thread now, but just wondering if there were updates on this front.
Particularly, I am have a dataset where I have 3dAutomask-ed each individual's image to remove dropout regions. I was hoping to have this excluded person/voxel-wise in the group-level 3dLME - but it seems like it may be reading this in as zero values. I tried using the -bounds options but am getting an error (tested this a few ways but was aiming to use a lower bound of ~0.1 to remove any zeros where all valid values are positive in this case).
Example Script:
3dLMEr -prefix lme \
-jobs 4 -bounds .01 10 \
-mask MNI152_T1_2mm_brain_mask.nii \
-model 'Dx+Sex+age+(1|run)' \
-qVars 'age' -qVarCenters '0,' \
-gltCode ocd 'Dx : 1*OCD -1*Healthy' \
-dataTable @covars.txt
Error:
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++
Reading input files now...
Reading input files for effect estimates: Done!
Range of input data: [0.000, 3.748]
Input data confined within [0.01, 10]
If the program hangs here for more than, for example, half an hour,
kill the process because the model specification or something else
is likely inappropriate.
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
boundary (singular) fit: see ?isSingular
[1] "Great, test run passed at voxel (33, 33, 42)!"
[1] "Start to compute 91 slices along Z axis. You can monitor the progress"
[1] "and estimate the total run time as shown below."
[1] "05/13/21 14:19:17.469"
Loading required package: snow
Package snow loaded successfully!
Error in checkForRemoteErrors(val) :
4 nodes produced errors; first error: missing value where TRUE/FALSE needed
Calls: aperm ... clusterApply -> staticClusterApply -> checkForRemoteErrors
Execution halted
