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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.
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:
Pitzer
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:
Pitzer
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:
Pitzer
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.
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:
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.
We have licensed applications such as ansys, abaqus, and Schrodinger. These applications have a license server with a limited number of licenses, and you need to check out the licenses when you use the software each time. One problem is that the job scheduler, Slurm, doesn't communicate with the license server. As a result, a job can be launched even there are not enough licenses available, and it fails due to insufficient licenses.
Charge account
- Used to group projects together.
- A PI may have multiple charge accounts, but it is preferred to limit the amount to one unless there is reason to group different projects.
- Institutions may use charge accounts to group PI charge accounts together
- (e.g. group all college of engineering PI charge accounts under college of engineering charge account)