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Cardinal, Pitzer
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.
Ascend
SCIPION is an image processing framework fo robtaining 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents a unified interface for both biologists and developers. Scipion allows you to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on.
Pitzer
rclone is a tool that can be used to upload and download files to a cloud storage (like Microsoft OneDrive, BuckeyeBox) from the command line. It's shipped as a standalone binary, but requires some user configuration before using. In this page, we will provide instructions on how to use rclone to upload data to OneDrive. For instructions with other cloud storage, check rclone Online documentation.
Pitzer
SPM is made freely available to the [neuro]imaging community, to promote collaboration and a common analysis scheme across laboratories. The software represents the implementation of the theoretical concepts of Statistical Parametric Mapping in a complete analysis package.
Ascend, Cardinal, Pitzer
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.
Gateway
MyOSC now supports multi-factor authentication (MFA).
User opt-in
Users can now opt-in to using multi-factor authentication in MyOSC.
On a user's profile page, there will be a button Enable DUO MFA.
Ascend, Cardinal, Pitzer
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:
Ascend, Cardinal, Pitzer
DSI Studio is a tractography software tool that maps brain connections and correlates findings with neuropsychological disorders.
Ascend, Cardinal, Pitzer
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:
Ascend, Cardinal, Pitzer
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.
