Neuropointillist is an in-development R package which defines functions to help scientists to run voxel-wise models using R neuroimaging data.
The following versions are available on OSC clusters:
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 is a program that provides automatic prediction of quality and visual reporting of MRI scans.
The following versions are available on OSC clusters:
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.
Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
The following versions of Trinity are available on OSC clusters:
There are different ways to submit interactive jobs.
sinteractiveYou can use the custom tool sinteractive as:
| Use | Torque/Moab Command | Slurm Equivalent |
|---|---|---|
| Submit batch job | qsub <jobscript> |
sbatch <jobscript> |
| Submit interactive job | qsub -I [options] |
|
It is possible to utilize Cron and the OSCusage command to send regular usage reports via email
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.
An ACL (access control list) is a list of permissions associated with a file or directory. These permissions allow you to restrict access to a certain file or directory by user or group.
OSC supports NFSv4 ACL on our home directory and POSIX ACL on our project and scratch file systems. Please see the how to use NFSv4 ACL for home directory ACL management and how to use POSIX ACL for managing ACLs in project and scratch file systems.
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.
