![UWO-BrainsCAN-Logo][1]
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# 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.
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## Experiment Development Tools
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## 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.
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## Resources
### Linux commands
New users can find a list of frequently used linux commands [here][14].
### Software websites and message boards
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## 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
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## 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/