Page Index - CoBrALab/documentation GitHub Wiki

253 page(s) in this GitHub Wiki:

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