Software

AFNI

AFNI (Analysis of Functional Neuro Images) is a leading software suite of C, Python, and R programs and shell scripst primarily developed for the analysis and display of multiple MRI modalities: anatomical, functional MRI (FMRI) and diffusion wieghted (DW) data. It is freely available (both as open source code and as precompiled binaries) for research purposes.

Availability and Restrictions

Versions

The following versions are available on OSC clusters:

Neuropointillist

Neuropointillist is an in-development R package which defines functions to help scientists to run voxel-wise models using R neuroimaging data.

Availability and Restrictions

Versions

The following versions are available on OSC clusters:

xcpEngine

The XCP imaging pipeline (XCP system) is a free, open-source software package for processing of multimodal neuroimages. The XCP system uses a modular design to deploy analytic routines from leading MRI analysis platforms, including FSL, AFNI, and ANTs.

Availability and Restrictions

Versions

xcpEngine is available on Pitzer cluster. These are the versions currently available:

Connectome

Connectome is an open-source visualization and discovery tool used to explore data generated by the Human Connectome Project. The distribution includes wb_view, a GUI-based visualization platform, and wb_command, a command-line program for performing a variety of algorithmic tasks using volume, surface, and grayordinate data.

Availability and Restrictions

Versions

The following versions are available on OSC clusters:

DSI Studio

DSI Studio is a tractography software tool that maps brain connections and correlates findings with neuropsychological disorders. It is a collective implementation of several diffusion MRI methods, including diffusion tensor imaging (DTI), generalized q-sampling imaging (GQI), q-space diffeomorphic reconstruction (QSDR), diffusion MRI connectometry, and generalized deterministic fiber tracking.

MRIQC

MRIQC is a program that provides automatic prediction of quality and visual reporting of MRI scans.

Availability and Restrictions

Versions

The following versions are available on OSC clusters:

fMRIPrep

fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.

Trinity

Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.

Availability and Restrictions

The following versions of Trinity are available on OSC clusters:

PETSc

PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It supports MPI, and GPUs through CUDA or OpenCL, as well as hybrid MPI-GPU parallelism.

Software Refresh - May 2020

OSC will be refreshing the software stack for Owens and Pitzer on May 19, 2020. This will be done in a system-wide downtime. During the software refresh, some default versions will be changed to be more up-to-date. Information about the new default versions, as well as all available versions of each software package will be included on the corresponding OSC software webpage. See https://www.osc.edu/supercomputing/software-list.

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