Cardinal

Texlive

TeX Live is a straightforward way to get up and running with the TeX document production system. It provides a comprehensive TeX system with binaries for most flavors of Unix, including GNU/Linux, macOS, and also Windows. It includes all the major TeX-related programs, macro pacakges, and fonts that are free software, including support for many languages around the world.

Availability and Restrictions

Versions

The following versions are available on OSC clusters:

HOWTO: Use Extensions with JupyterLab

JupyterLab stores the main build of JupyterLab with associated data, including extensions in Application Directory. The default Application Directory is the JupyterLab installation directory where is read-only for OSC users. Unlike Jupyter Notebook, JupyterLab cannot accommodate multiple paths for extensions management. Therefore we set the user's home directory for Application Directory so as to allow user to manage extensions.

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:

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.

HOWTO: Use Cron and OSCusage for Regular Emailed Reports

It is possible to utilize Cron and the OSCusage command to send regular usage reports via email

Cron

It is easy to create Cron jobs on the Cardinal and Pitzer clusters at OSC. Cron is a Linux utility which allows the user to schedule a command or script to run automatically at a specific date and time. A cron job is the task that is scheduled.

Shell scripts run as a cron job are usually used to update and modify files or databases; however, they can perform other tasks, for example a cron job can send an email notification.

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