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Welcome to the wiki of the MICA-lab. This page contains the repository for the wiki and important information.

We encourage you to support the development of this wiki in the following ways:

1. Adding or correcting any entry that is already in the wiki.
2. Including anything new that others can learn and use it too.
3. ⚠️ How-to create a Wiki entry

Home Content

1. Arrival and How-to
2. Data Acquisition
3. Data Processing
4. Data Analysis
5. MICA ecosystem
6. FAQ

Arrival and How-to

• Arrival how to get SIN, McGill Registration, BIC account, GitHub username, slack membership
• MUHC id, OASIC access permission and MUHC computer access.
• Booking rooms or volunteers
• Phone Phone numbers
• Remote access to MICA workstations
• Computing computing at the BIC
• Fellowships and Awards Rake in that sweet dough

Data Acquisition

• MICA 3T protocol description of the scanning we do and the parameters
• MICA 3T Task setup descriptions of how to run the tasks
• MICA 7T protocol description of the scanning parameters
• MICA PET MK-6240 protocol description of the scanning parameters

Datasets

• MICs the 3T non-task imaging acquisitions in healthy and epileptic individuals
• MICA-SPM the 3T task acquisitions in healthy and epileptic individuals
• MICA-PET the PET MK-6240 data in healthy and epileptic individuals
• HCP the Human Connectome Project S900 release (3T)
• HCP7T the 7T subset of the HCP
• ABIDE ABIDE-1 and ABIDE-2 subsets preprocessed and QC-ed in the lab
• HCP-d HCP development (children)
• d-HCP dHCP (babies)
• HBN Healthy Brain Network dataset
• Vancouver The UBC-MNI dataset
• EpiC The epilepsy and cognition dataset from UNAM Mexico.
• BigMac a resource combining in vivo MRI, extensive postmortem MRI and multi-contrast microscopy for multimodal characterisation of a single whole macaque brain

Data Processing - Pipelines

• Bash + queue 101
• Dicoms to BIDS
• micapipe
• Freesurfer processing
• Surfpatch processing
• Hipunfold
• Superficial white matter processing
• Tractography processing
• Task fMRI processing
• PET processing

Data Analysis

• Surfstat web page Webpage also available under http://mica-mni.github.io/surfstat. SurfStat allows for statistical analysis of surface and volumetric data using univariate and multivariate GLMs, linear mixed effects models, and random field theory. A short pdf intro also available in http://github.com/MICA-MNI/micaopen (goto surfstat/surfstat_tutorial)

• BrainSpace web page, macroscale gradient mapping and analysis of neuroimaging and connectome level data.

• SPHARM web page, subcortical mesh data processing pipeline.

• Network analysis (https://sites.google.com/site/bctnet/), graph theoretical tools

• Dynamic functional analysis Hidden Markov Models

• MPC, Microstructure profile covariance scripts

• Allen brain transcriptomic decoding correlate surface based maps with gene expressions

• Neurosynth decoding correlate surface based maps with psychological terms

MICA ecosystem

• BrainSpace

• Enigma toolbox

• Big Brain Warp

• BrainStat

• micapipe

FAQ

• Github How to create an entry?, How to branch?, How to change commit History?