Usage in LONI

There are a set of shell script wrappers for the command line pipeline modules that were developed for running the pipelines in parallel on the computing cluster here at CCHMC.


Although, these are provided for reference within the source code distribution within the /site_specific/LONI_shell folder, they are not expected to work as is in other cluster environments without some manual editing. In particular many of the shell scripts call utilities such as which tries to a module containing FSL in the cluster. The particulars of loading each software package in load_*.sh would have to be updated to reflect the local software environment. Additionally, some paths and variables may be hardcoded to values appropriate to the C-MIND study, but may not apply to other studies.

Reference LONI .pipe files containing the full physiological and functional session pipelines that were run via the cluster to generate the files in the database are available in the source distribution within the folder: cmind-py/study_specific/LONI_pipelines