Installation

sMRIPost-LINC should be installed using container technologies.

Containerized execution (Docker and Singularity)

sMRIPost-LINC is a NiPreps application, and therefore follows some overarching principles of containerized execution drawn from the BIDS-Apps protocols. For detailed information of containerized execution of NiPreps, please visit the corresponding Docker or Singularity subsections.

External Dependencies

sMRIPost-LINC is written using Python 3.8 (or above), and is based on nipype.

sMRIPost-LINC requires some other neuroimaging software tools that are not handled by the Python’s packaging system (Pypi):

• FSL (version 6.0.7.7)

• ANTs (version 2.5.1)

• AFNI (version 24.0.05)

• C3D (version 1.4.0)

• FreeSurfer (version 7.3.2)

• bids-validator (version 1.14.0)

• connectome-workbench (version 1.5.0)

Not running on a local machine? - Data transfer

If you intend to run sMRIPost-LINC on a remote system, you will need to make your data available within that system first.

For instance, here at the Poldrack Lab we use Stanford’s HPC system, called Sherlock. Sherlock enables the following data transfer options.

Alternatively, more comprehensive solutions such as Datalad will handle data transfers with the appropriate settings and commands. Datalad also performs version control over your data.