Hi AFNI experts,

I am running 3dLME on high resolution data that only covers a portion of the brain. I am using the -mask option to reduce the time and resources it will take, using this command:

3dLME -prefix Rest_LME -model "Cond*Side" \
-ranEff "~1" -SS_type 3 \
-jobs 6 \
-mask ./groupmask_all+tlrc \
-num_glt 6 \
-gltLabel 1 'Threat m Safe' \
-gltCode 1 'Cond : 1*T -1*S' \
-gltLabel 2 'LmR' \
-gltCode 2 'Side : 1*L -1*R' \
-gltLabel 3 'TmS in L' \
-gltCode 3 'Cond : 1*T -1*S Side : 1*L' \
-gltLabel 4 'TmS in R' \
-gltCode 4 'Cond : 1*T -1*S Side : 1*R' \
-gltLabel 5 'LmR in Safe' \
-gltCode 5 'Side : 1*L -1*R Cond : 1*S' \
-gltLabel 6 'LmR in Threat' \
-gltCode 6 'Side : 1*L -1*R Cond : 1*T' \
-dataTable \
Subj Cond Side IPIP_Extravers IPIP_Agreeable IPIP_Conscient IPIP_Intellect BIS_TOTAL BAS_RS BAS_Drive BAS_SS BAS_TOTAL EC_tot SC_tot PolAffil CESD_Total \
RSS_TOTAL Sens2Reward Sens2Punish SPIN_TOTAL BAI_TOTAL CSRI_TOTAL RSRI_TOTAL IUS_TOTAL PSWQ_TOTAL STAITrait_TOTAL_MRsess InputFile \
2202 T L 16 15 13 11 14 17 12 11 40 13 8 1 8 30 7 1 1 3 54 40 46 43 34 /bigraid-03/LS/Data/7T_BNST/afni/subs/2202/rest/results_restT_MNIb2/LBNST_Tzmap+tlrc \
2202 T R 16 15 13 11 14 17 12 11 40 13 8 1 8 30 7 1 1 3 54 40 46 43 34 /bigraid-03/LS/Data/7T_BNST/afni/subs/2202/rest/results_restT_MNIb2/RBNST_Tzmap+tlrc \
...

When I run this command, the output gets to:

Reading input files now... 
Reading input files: Done! 

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. 

[1] "Great, test run passed at voxel (75, 133, 112)!" 
[1] "Start to compute 225 slices along Z axis. You can monitor the progress" 
[1] "and estimate the total run time as shown below." 
[1] "10/06/16 11:06:36.369" Loading required package: snow Package snow loaded successfully!

And then does not progress, even after a few hours. However, if I comment out the -mask option, the program moves on after about 15 minutes and starts going through slices, with output like:

Z slice 1 done: 10/06/16 12:35:25.228
...

I've checked the mask that I am using - it is in the same space as my data, and is made up of only ones and zeros.

Anyone know what I could do to get the -mask option working?

Thanks!