Loading wiki pages...

Wiki Version:
<p><img alt="UWO-BrainsCAN-Logo" src="https://files.osf.io/v1/resources/k89fh/providers/osfstorage/5c8bcaa818184e0018bf7753?mode=render"></p> <hr> <h1>BrainsCAN Computational Core Neuroimaging Wiki</h1> <p>@[toc]</p> <h2>Tools for fMRI data</h2> <h3>autobids</h3> <p><a href="https://osf.io/k89fh/wiki/autobids/" rel="nofollow">Autobids</a> is a platform for automated download, standardization, and post-processing of neuroimaging data using the BIDS standard.</p> <h3>correct 7T pipeline</h3> <p>The <a href="https://osf.io/k89fh/wiki/correct%207T%20pipeline/" rel="nofollow">correct 7T pipeline</a> is a post-BIDS conversion set of tools for running standard corrections and QC tools for MRI data collected on the CFMM 7T scanner.</p> <h3>3T post-processing pipeline</h3> <p>The postproc 3T pipeline is a post-BIDS conversion sets of tools for running standard corrections and QC tools for MRI data collected on the CFMM 3T scanner.</p> <h3>BIDS apps</h3> <p>The BrainsCAN Computational Core and the Khan Lab support users in a number of <a href="https://osf.io/k89fh/wiki/BIDS%20apps/" rel="nofollow">BIDS apps</a>.</p> <h3>fmriprep-docker</h3> <p><a href="https://osf.io/k89fh/wiki/fmriprep-docker/" rel="nofollow">fmriprep-docker</a> is a light-weight wrapper for the BIDS app fmriprep.</p> <h3>neuroglia-helpers</h3> <p><a href="https://osf.io/k89fh/wiki/neuroglia-helpers/" rel="nofollow">neuroglia-helpers</a> is a set of wrapper scripts provided by the Khan Lab to faciliate SLURM job submission on Compute Canada. The scripts are particularly useful for submitting BIDS app jobs. </p> <h3>physIO</h3> <p><a href="https://osf.io/k89fh/wiki/physIO/" rel="nofollow">physIO</a> is a SPM/Matlab-based toolbox for handling physiology recordings acquired during fMRI scans.</p> <h3>Surface Based Analysis</h3> <p><a href="https://osf.io/k89fh/wiki/Surface/" rel="nofollow">Surface-based analysis</a> of cortical MRI data using freesurfer and Connectome Workbench tools. </p> <h3>ISC Toolbox output</h3> <p>How to <a href="https://osf.io/k89fh/wiki/ISC%20Toolbox%20output/" rel="nofollow">fix</a> ISC toolbox output images so that they can be visualized as overlays on a template image.</p> <hr> <h2>Experiment Development Tools</h2> <hr> <h2>Computation Tools</h2> <h3>Computational Data Science Group Server</h3> <p>The <a href="https://osf.io/k89fh/wiki/Computational%20Core%20Server/" rel="nofollow">BMI Server</a> is a new high performance compute system jointly managed by Robarts and the BrainsCAN Computational Core. </p> <h3>Compute Canada</h3> <p><a href="https://osf.io/k89fh/wiki/Compute%20Canada/" rel="nofollow">Compute Canada</a> is a federally funded high-performance compute (HPC) system.</p> <h3>Singularity</h3> <p><a href="https://osf.io/k89fh/wiki/Singularity/" rel="nofollow">Singularity</a> is a container based solution for sharing softwares and libraries.</p> <h3>Docker</h3> <p><a href="https://osf.io/k89fh/wiki/Docker/" rel="nofollow">Docker</a> is a container based solution for sharing software and libraries.</p> <hr> <h2>Resources</h2> <h3>Linux commands</h3> <p>New users can find a list of frequently used linux commands <a href="https://osf.io/k89fh/wiki/Linux%20commands/" rel="nofollow">here</a>.</p> <h3>Software websites and message boards</h3> <hr> <h2>CFMM - MRI scanning information</h2> <p>Homepage: <a href="https://cfmm.uwo.ca" rel="nofollow">https://cfmm.uwo.ca</a></p> <p>Safety training: <a href="https://cfmm.uwo.ca/resources/safety.html" rel="nofollow">https://cfmm.uwo.ca/resources/safety.html</a></p> <p>MRI scanning standard operating procedures: <a href="https://cfmm.uwo.ca/resources/sops.html" rel="nofollow">https://cfmm.uwo.ca/resources/sops.html</a></p> <p>Forms: <a href="https://cfmm.uwo.ca/resources/forms.html" rel="nofollow">https://cfmm.uwo.ca/resources/forms.html</a></p> <hr> <h2>fNIRS</h2> <p>Details coming...</p>
OSF does not support the use of Internet Explorer. For optimal performance, please switch to another browser.
This website relies on cookies to help provide a better user experience. By clicking Accept or continuing to use the site, you agree. For more information, see our Privacy Policy and information on cookie use.

Start managing your projects on the OSF today.

Free and easy to use, the Open Science Framework supports the entire research lifecycle: planning, execution, reporting, archiving, and discovery.