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:
Ascend
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.
Steps on How to Submit Jobs
How to Submit Interactive jobs
There are different ways to submit interactive jobs.
Using sinteractive
You can use the custom tool sinteractive as:
How to Submit, Monitor and Manage Jobs
Submit Jobs
| Use | Torque/Moab Command | Slurm Equivalent |
|---|---|---|
| Submit batch job | qsub <jobscript> |
sbatch <jobscript> |
| Submit interactive job | qsub -I [options] |
|
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.
Manage profile information
Edit profile
Profile information can be changed by logging in with valid OSC credentials at MyOSC, navigating to the profile page by clicking the display name in the upper right corner of the page, and selecting Edit my profile.
OSC Classroom Support
CLASSROOM RESOURCES FOR DISTANCE LEARNING
If your class has lost or limited access to computer labs, the Ohio Supercomputer Center might be able to help by providing no-cost access to cloud computing resources. Classes and workloads of any size can gain access. OSC's web-browser interface to its substantial Linux computer systems provides novice users with virtual desktops preloaded with applications, such as MATLAB, RStudio, or Jupyter Notebook.
As an example, an OSU undergrad statistics class recently used iPads to remotely access RStudio on OSC systems.
Connectome Workbench
Connectome Workbench is an open source, freely available visualization and analysis tool for neuroimaging data, especially data generated by the Human Connectome Project.
Availability and Restrictions
Versions
Connectome Workbench is available on Pitzer and Cardinal clusters. These are the versions currently available:
Gaussian
Gaussian is a very popular general purpose electronic structure program. Recent versions can perform density functional theory, Hartree-Fock, Möller-Plesset, coupled-cluster, and configuration interaction calculations among others. Geometry optimizations, vibrational frequencies, magnetic properties, and solution modeling are available. It performs well as black-box software on closed-shell ground state systems.
HOW TO: Look at requested time accuracy using XDMoD
The XDMoD tool at xdmod.osc.edu can be used to get an overview of how accurate the requested time of jobs are with the elapsed time of jobs.
To request an amount of time for a job, you can use the following header.
#SBATCH --time=xx:xx:xx
The elapsed time is how long the job ran for before completing. This can be obtained for completed jobs using the sacct command.
