Pitzer
HOWTO: Use 'rclone' to Upload Data
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.
SPM
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.
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:
System Downtime June 30, 2021
A downtime for all OSC HPC systems is scheduled from 7 a.m. to 9 p.m., Wednesday, June 30, 2021. The downtime will affect the Pitzer and Owens Clusters, web portals, state-wide licenses, and HPC file servers. Login services will not be available during this time. Client portal (my.osc.edu) will be accessible.
In preparation for the downtime, jobs that cannot be completed before 7 a.m., June 30, 2021 will not start. Jobs that are not started on clusters will remain until after the downtime and then will be queued to start once the system is returned to production status.
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:
Problems with GPFS filesystem
We are experiencing some problems with GPFS filesystems this morning (Thursday, June 10). OnDemand is not working. It may also cause unexpected job failures. We are working hard to fix this issue, and will provide more updates once we know more. See this page: https://www.osc.edu/resources/technical_support/known_issues/problems_with_gpfs_filesystem_and_ondemand_is_not_working
