It can take quite a while sometimes. There should be a directory called "csd" with a file in there for your contrast. If you look in there, it will tell you how many interactions it has completed. Also, make sure that you have only one contrast as there is a bug with multiple contrasts. Also, if you have a computer with multiple cores, you can split the jobs up and run it in parallel with --bg. Make sure to read the help for --bg. If you use this option and then just kill the job, the processes will continue to run in the background. There are instructions there on how to cleanly shut it down.

doug

Antonella Kis wrote:

Hi Doug,

I wonder how many hours it can take the mri_glmfit-sim with perm option. This is what I was running yesterday from 2 pm and is still not completed. It can take so long or there may be something wrong? I did not get any error but I have the same number of files as yesterday in my GroupAnalysis.glmdir. I also attached my log file.

mri_glmfit-sim \ --glmdir Group_Analysis.glmdir \ --sim perm 10000 3 permcsd \ --sim-sign neg \ --cwpvalthresh .05

Thank you for any suggestion and help. Antonella