<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>