Installation

Python Environment Setup

If you have priviledges to add python packages to a system, you can install the most recent version of clpipe with:

pip3 install --upgrade git+https://github.com/cohenlabUNC/clpipe.git

If you don’t have access to the global library (perhaps you are just a user of an HPC), you can install a local copy by adding the --user flag:

pip3 install --user --upgrade git+https://github.com/cohenlabUNC/clpipe.git

Pip will automatically install all required Python package dependencies.

External Dependencies

If you don’t already have a Singularity image of fMRIprep, head over to their site and follow the directions. You will have to change the fMRIprep image path in your configuration file.

Similarly, if you do not have a copy of the BIDS-validator Singularity image, you’ll need to obtain this image as well:

Additionally, clpipe requires the following tools to be installed in order to run its postprocessing and analysis steps (UNC-CH Users - this is handled by the clpipe module):

  • FSL (recommended v6.0.0 +)

  • AFNI (recommended v20.0.00 +)

  • R (v4.0.0 +)

A Note for UNC-CH Users

If you are a Longleaf user and a member of the hng posix group, clpipe has already been installed for you via the module system. Add the following line to your ~/.bashrc file to include clpipe’s modules:

module use /proj/hng/software/modules

You can then use the following to access the latest version of clpipe:

module add clpipe

You also already have access to the latest singularity images for both fmriprep and the bids validator at /proj/hng/singularity_imgs, so there is no need to construct your own, unless you want a older version.

Batch Languages

clpipe was originally designed for use on the University of North Carolina at Chapel Hill’s HPC, Longleaf, which uses the SLURM task management system. The way clpipe handles what batch language to use is through a set of batch configuration files. These files are not directly exposed to users, and modification of these directly is ill advised. For other institutions that use task management systems other than SLURM, get in touch with the package maintainers, and we would be happy to help setup a configuration file for your system. In coming versions of clpipe, functionality will be added to allow users to change the batch management system settings.