![UWO-BrainsCAN-Logo][1] ---------- # BrainsCAN Computational Core Neuroimaging Wiki @[toc] ## Tools for fMRI data ### autobids [Autobids][2] is a platform for automated download, standardization, and post-processing of neuroimaging data using the BIDS standard. ### correct 7T pipeline The [correct 7T pipeline][3] is a post-BIDS conversion set of tools for running standard corrections and QC tools for MRI data collected on the CFMM 7T scanner. ### 3T post-processing pipeline 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. ### BIDS apps The BrainsCAN Computational Core and the Khan Lab support users in a number of [BIDS apps][4]. ### fmriprep-docker [fmriprep-docker][5] is a light-weight wrapper for the BIDS app fmriprep. ### neuroglia-helpers [neuroglia-helpers][6] 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. ### physIO [physIO][7] is a SPM/Matlab-based toolbox for handling physiology recordings acquired during fMRI scans. ### Surface Based Analysis [Surface-based analysis][8] of cortical MRI data using freesurfer and Connectome Workbench tools. ### ISC Toolbox output How to [fix][9] ISC toolbox output images so that they can be visualized as overlays on a template image. ---------- ## Experiment Development Tools ---------- ## Computation Tools ### Computational Data Science Group Server The [BMI Server][10] is a new high performance compute system jointly managed by Robarts and the BrainsCAN Computational Core. ### Compute Canada [Compute Canada][11] is a federally funded high-performance compute (HPC) system. ### Singularity [Singularity][12] is a container based solution for sharing softwares and libraries. ### Docker [Docker][13] is a container based solution for sharing software and libraries. ---------- ## Resources ### Linux commands New users can find a list of frequently used linux commands [here][14]. ### Software websites and message boards ---------- ## CFMM - MRI scanning information Homepage: https://cfmm.uwo.ca Safety training: https://cfmm.uwo.ca/resources/safety.html MRI scanning standard operating procedures: https://cfmm.uwo.ca/resources/sops.html Forms: https://cfmm.uwo.ca/resources/forms.html ---------- ## fNIRS Details coming... [1]: https://files.osf.io/v1/resources/k89fh/providers/osfstorage/5c8bcaa818184e0018bf7753?mode=render [2]: https://osf.io/k89fh/wiki/autobids/ [3]: https://osf.io/k89fh/wiki/correct%207T%20pipeline/ [4]: https://osf.io/k89fh/wiki/BIDS%20apps/ [5]: https://osf.io/k89fh/wiki/fmriprep-docker/ [6]: https://osf.io/k89fh/wiki/neuroglia-helpers/ [7]: https://osf.io/k89fh/wiki/physIO/ [8]: https://osf.io/k89fh/wiki/Surface/ [9]: https://osf.io/k89fh/wiki/ISC%20Toolbox%20output/ [10]: https://osf.io/k89fh/wiki/Computational%20Core%20Server/ [11]: https://osf.io/k89fh/wiki/Compute%20Canada/ [12]: https://osf.io/k89fh/wiki/Singularity/ [13]: https://osf.io/k89fh/wiki/Docker/ [14]: https://osf.io/k89fh/wiki/Linux%20commands/