Description:
I’m trying to process the HCP example data using the qunex docker container but it seems that run_turnkey fails when it gets to the hcp_fmri_volume pipeline. The error is not fatal in that the code continues to run through hcp_fmri_surface but it doesn’t produce anything. Can anyone see what the issue is? I’m following these instructions. Please let me know if there is any additional information I can provide to clarify the issue.
Welcome to QuNex forums! It seems like something went wrong inside hcp_fmri_volume. It would be helpful for us to diagnose if you could share the log file for hcp_fmri_volume with us. It should be something like this [tmp/done/error]_hcp_fmri_volume_2_HCPA001_2021-09-17_17.19.1631913585.log in comlog folder. Or you can zip the log folder, if it’s easier for you.
Right now I have qunex installed at /usr/local/qunex. Our server has a small amount of storage allocated to the root directory (/usr/local, /home, etc) with 12TB of attached storage mounted at /bcdlab. Could I keep qunex installed in the root directory but have the all of the actual data in the mounted storage? In other words, can I keep /usr/local/qunex but move /data to /bcdlab and have all qunex outputs written to /bcdlab?
Certainly, you can do that. You just need to change --bind for singularity or --dockeropt for docker to change what host directories are mapped into the container.