How to create Parameter, Batch and Mapping Files for HCP data that was preprocessed outside of Qunex

Hello, we’re trying to just use Qunex to run hcp_icafix on HCP that has already been minimally preprocessed. We ran create_study to create the necessary Qunex folders, and then copied our preprocessed data into the /StudyFolder/sessions/SubID/hcp/SubID folder.

When we try to run hcp_icafix with the following command:

/cm/shared/qunex_container hcp_icafix --sessionsfolder=“/data/ckorponay/qunex/HCP/sessions/100408” --container=“/data/singularity-images/qunex_suite-0.95.3a.sif” --bind=“/data:/data” --hcp_icafix_bolds=“tfMRI_WM_LR”

It doesn’t seem like anything happens. I’m assuming that’s because we’re missing the parameter, batch, and/or mapping files. How would we create those for this purpose?


  1. You just need to prepare the batch file. Attached is an example based on two sessions from the HCA dataset.

batch.txt (14.9 KB)

  1. Alternatively, until we fix this, you could bypass QuNex and use the container to directly run HCP Pipelines with it. To do this follow the instructions below:
# enter the container
singularity shell -B /data:/data /data/singularity-images/qunex_suite-0.95.3a.sif

# source QX environment to load all the tools
source /opt/qunex/env/

# HCP ICAFix and all its scripts are now accessible at

# run HCP ICAFix directly