Page Index - CoBrALab/documentation GitHub Wiki

245 page(s) in this GitHub Wiki:

• Home
• 3D visualization of stat files for mice
• Please reload this page
• AAL Atlas
• Please reload this page
• Allen Brain Adult Mouse
• Please reload this page
• ANTS transforms on volume (MNC, NIFTI) and surface (OBJ) files
• Please reload this page
• Automated Visualization of mincLm and mincLmer Models
• Please reload this page
• Automatically label peak voxels from mincLM LMER with an atlas
• Please reload this page
• Average Thickness and Surface Area from AAL atlas CIVET
• Please reload this page
• Best Practices for Standardized Quality Control (QC) and Quality Assurance (QA)
• Please reload this page
• Best Templates for MAGeT
• Please reload this page
• bruker2nifti conversion
• Please reload this page
• CIVET Quality Control Guidelines
• Please reload this page
• CoBrALab Cookbook
• Please reload this page
• Computing local gyrification from CIVET outputs
• Please reload this page
• Converting a Single Coordinate from Paxinos to DSURQE to Allen
• Please reload this page
• Converting dicom to minc
• Please reload this page
• Cortical Thickness & Surface Analysis with CIVET
• Please reload this page
• Create 3D surfaces using Mango
• Please reload this page
• Create a nifti of within subject change (2 timepoints, output from dbm)
• Please reload this page
• Cross‐site data harmonization using CovBat in Python
• Please reload this page
• dbm on Trillium
• Please reload this page
• Demographically Stratified Templates for MAGeTbrain
• Please reload this page
• DEPRECATED ANTs Multivariate Template Construction
• Please reload this page
• DEPRECATED pydpiper: Running MBM.py on cross sectional data
• Please reload this page
• DEPRECATED pydpiper: Running MBM.py without a target atlas
• Please reload this page
• DEPRECATED: automated QC of raw images
• Please reload this page
• DEPRECATED: CIVET 2.1.0 on Niagara
• Please reload this page
• DEPRECATED: Guide to using lpba40 to calculate mean cortical thickness and surface area
• Please reload this page
• DEPRECATED: How to run MICe build model on Niagara
• Please reload this page
• Display mnc files from the terminal
• Please reload this page
• Downsampling Objects in Amira
• Please reload this page
• DSURQE atlas hierarchical downsample
• Please reload this page
• Embryo scan preprocessing
• Please reload this page
• Extracting Grey Matter, White Matter, and CSF volume measures from CIVET
• Please reload this page
• Extraction of parcellated fMRI timeseries from the hierarchical downsampled DSURQE atlas
• Please reload this page
• Finding an optimal mixed effects model
• Please reload this page
• FreeSurfer for Thickness or Volume
• Please reload this page
• Generating MAGeTbrain Quality Control Images
• Please reload this page
• Getting Help
• Please reload this page
• Getting Images into the Wiki
• Please reload this page
• Getting Started on Niagara
• Please reload this page
• Getting started on Trillium
• Please reload this page
• Getting started with Béluga
• Please reload this page
• HCP Workbench Command Tips
• Please reload this page
• How to analyze raw USV data
• Please reload this page
• How to impute missing data a data matrix using SVD
• Please reload this page
• How to run MAGeT for mouse brains on the CIC cluster or Niagara
• Please reload this page
• HPSS (Archive) Storage on SciNet
• Please reload this page
• Impute Missing Data Using XGBoost: mixgb
• Please reload this page
• Introduction to resting state fMRI and functional connectivity analysis
• Please reload this page
• Introduction to using Terminal and Display for Segmenting the Hippocampus
• Please reload this page
• MAGeT Brain Quality Control (QC) Guide
• Please reload this page
• MAGeT Brain Related Masking
• Please reload this page
• MAGeT for highres isotropic T2w and slab anisotropic scans
• Please reload this page
• MAGeTBrain
• Please reload this page
• MAGeTbrain Morphology
• Please reload this page
• Making a stats mask for 2level dbm output
• Please reload this page
• Managing jobs on SGE (Sun Grid Engine)
• Please reload this page
• Mapping Anatomical Correlations Across Cerebral Cortex (MACACC Method)
• Please reload this page
• Morris Water Maze
• Please reload this page
• Motion Quality Control (QC) Manual
• Please reload this page
• Mouse DICOM to MINC Conversion
• Please reload this page
• Mouse QC Manual (Structural)
• Please reload this page
• Mouse Scan Preprocessing
• Please reload this page
• MRS Preprocessing and Basis Set Creation Using FID A and Analysis Using LCModel
• Please reload this page
• Myelin Imaging via Magnetization Transfer (MTR)
• Please reload this page
• Neonate Scanning (Work In Progress)
• Please reload this page
• New Lab Member Reading (Onboarding)
• Please reload this page
• NMF in R
• Please reload this page
• Non linear registration doesn't matter (much) or how I learned to stop worrying and love the affine
• Please reload this page
• Open Field Task
• Please reload this page
• opNMF for vertex data
• Please reload this page
• Power Analysis
• Please reload this page
• Preprocess Rat brains
• Please reload this page
• Project Data Organization
• Please reload this page
• Properly plotting an lm or lmer model predicted curve in R with ggplot
• Please reload this page
• pydpiper: Introduction to twolevel_model_building.py (old)
• Please reload this page
• pydpiper: Running MAGeT.py on longitudinal data
• Please reload this page
• QC and fix MRIs converted from other formats
• Please reload this page
• R Tips and Tricks
• Please reload this page
• References for commonly used techniques
• Please reload this page
• Resample image to a lower resolution
• Please reload this page
• Resting State fMRI Preprocessing Pipeline (work in progress)
• Please reload this page
• Roadmap to DBM analysis (mice)
• Please reload this page
• Rodent fMRI ‐ Generating Seeds for Seed Based Connectivity
• Please reload this page
• Rodent fMRI ‐ gICA & DR: Processing & Visualization
• Please reload this page
• Rodent fMRI‐ Functional Connectivity Between Networks or Regions
• Please reload this page
• ROI Analysis in CIVET
• Please reload this page
• Run things in parallel from R
• Please reload this page
• Running BIDS apps on Niagara
• Please reload this page
• Running fmriprep with singularity
• Please reload this page
• Running interactive MATLAB jobs on the cluster
• Please reload this page
• Running MATLAB PLS and SPM jobs on the cluster
• Please reload this page
• Running mincLmer on Niagara
• Please reload this page
• Running multiple MATLAB cluster pools as a single user
• Please reload this page
• Running PLS in MATLAB with cross sectional data
• Please reload this page
• Running PLS in Python: pyls
• Please reload this page
• Running python PLS on voxelwise data and normalizing Jacobians
• Please reload this page
• Running RABIES on niagara
• Please reload this page
• Running twolevel_ants_dbm on Niagara (old)
• Please reload this page
• Scanning Protocol MC4
• Please reload this page
• Scanning Protocol SML
• Please reload this page
• Software Quarantine at the CIC
• Please reload this page
• Spin test
• Please reload this page
• Submitting DBM jobs efficiently with Niagara
• Please reload this page
• Submitting jobs to the cluster with R
• Please reload this page
• Super resolution of MRI images
• Please reload this page
• Surface Sampling Using CIVET 2.x surfaces
• Please reload this page
• Surface Sampling Using CIVET surfaces
• Please reload this page
• Synthstrip_n3 on Trillium
• Please reload this page
• T1w T2w Ratio
• Please reload this page
• T2 and ADNI slab images preprocessing
• Please reload this page
• UK Biobank
• Please reload this page
• Unmask CIVET 2 data in python
• Please reload this page
• Updating Github from Terminal
• Please reload this page
• Useful resources for presentations and publications
• Please reload this page
• uv ‐ python package and project manager
• Please reload this page
• Vertex wise best model
• Please reload this page
• Visualizing DBM results on Mouse Average
• Please reload this page
• Visualizing MAGeT Brain results on Mouse Average
• Please reload this page
• Voxel Based Morphometry VBM with CIVET
• Please reload this page
• Wavelet transform visualization python script
• Please reload this page
• White matter hyperintensity (WMH) segmentation
• Please reload this page