Welcome to NeuroDocs!

Getting Started

• Introduction

Preprocessing (fMRIprep)

• Preprocessing Overview
• Preproc Step 1: Data Organization
• Preproc Step 2: fMRIprep
• Preproc Step 3: Brain Extraction

Task Analysis (FSL)

• Task Analysis Step 1: Timing Files

Preprocessing (CBIG2016)

• CBIG2016 Preprocessing Overview
• CBIG2016 Preproc Step 0
• CBIG2016 Preproc Step 1
• CBIG2016 Preproc Step 2
• CBIG2016 Preproc Step 3
• CBIG2016 Preproc: Tedana Integration

Parcellation (Kong2019)

• Kong2019 Parcellation Overview
• Kong2019 Parc Step 0
• Kong2019 Parc Step 1
• Kong2019 Parc Step 2
• Kong2019 Parc Step 3
• Kong2019 Parc Step 4
• Kong2019 Parc Step 5
• Kong2019 Parc: Training Your Own Priors

Parcellation (Kong2022)

• Kong2022 Parcellation Overview
• Kong2022 Step 0: Generate Gradients
• Kong2022 Step 1: Generate Profiles
• Kong2022 Step 2: Group Priors
• Kong2022 Step 3: Generate Individual Parcellations
• Kong2022 Step 4: Hungarian Matching and Visualization

Parcellation (K-means)

• K-means Parcellation Overview
• K-means Parc Step 1: Concatenate Timeseries
• K-means Parc Step 2: K-means Algorithm
• K-means Parc Step 3: Hungarian Matching and Visualization

Seed-based rsfMRI Analysis

• Seed-based rs-fMRI Analysis Overview
• Seed-based Analysis Step 1
• Seed-based Analysis Step 2
• Seed-based Analysis Step 3
• Seed-based Analysis Step 4
• Seed-based Analysis Step 5

tSNR Maps

• tSNR Maps Overview
• tSNR Step 1: tSNR Calculation
• tSNR Step 2: Surface Projection
• tSNR Step 3: Within-Network Averaging
• tSNR Step 4: Group-Averaged tSNR Map

Odds and Ends

• Implementing AWS CLI
• Installing Freesurfer
• Installing Conda
• Using MATLAB in a Supercomputing Environment
• Download a Dataset from OpenNeuro
• Overlap Map Figure
• Rclone
• Reorient a Nifti Image
• Read The Docs Documentation
• Split A BOLD Run
• Additional Resources