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