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Table of Contents

  • Atlases
    • How to Download and Install Additional FSL Atlases
    • BIP
    • HCP-MMP1 and HCP-MMP1_cortices
    • GreciusFunc
    • YeoBuckner7 and YeoBuckner17
  • BIDS
    • BIDS Containers
      • HeuDiConv
        • Introduction
        • Links
        • convertall.py
        • reproin.py
      • Introduction
        • BIDS Containers are BIG and Resource Intensive
        • Create Subdirectories under Derivatives for your Outputs
      • BET
        • Login to OOD and Get Ready
        • Use the Dataset on the HPC
        • Optional: Try Data Transfer
        • Prepare the Dataset
        • Build the BET Singularity Container
        • Run BET with Singularity
        • Understanding the Singularity Command
        • Running a Batch Job
        • Other Batch Scripts
      • BIP
        • Docker
        • Singularity
        • Job Times
      • DWIQC
        • Docker
        • Singularity
        • Job Times
      • fMRIPrep
        • Job Times
      • MRIQC
        • Docker
        • Singularity
        • Job Times
      • MRtrix3_connectome
        • Singularity
        • Job Times
    • Main Links
      • BIDS compatible datasets
    • Relevant Papers
    • Educational and Related Materials
    • Creating BIDS Datasets
      • bids-validator
        • Introduction
        • bids-validator online
        • Phasediff images
        • BIDS apps with narrow assumptions
        • Creating a .bidsignore
        • Example
      • HeuDiConv
        • Introduction
        • Links
        • convertall.py
        • reproin.py
  • Bookmarks
    • Brain Atlases
    • Computational Resources
    • fMRI Databases
    • Instructional: Neuroimaging Software and Concepts
    • MRI Concepts
    • Neuroimaging Tools
    • Other
  • Choropleth Visualization
    • Introduction
    • roixtractor
    • Resources
    • License
  • Glossary
  • Image Processing Tips and Tricks
    • Anatomical Image Preparation
      • Prepare T1w Image
      • fslreorient2std
      • Crop Neck with robustfov
      • Correct Extreme Anisotropy
      • Reslice Other Anatomicals into One Space
    • Masks
      • Erode
      • Dilate
      • Fill Holes
      • Cluster Count
      • Cluster Clean
      • Smooth
      • Left-Right Flip and Nudge
    • Check for Hidden Problems
      • fslinfo and fslhd
      • Ensure Zeros, not NaNs
      • Ensure SFORM and QFORM Match
      • Ensure Standard Orientation in NIFTI Header
      • Save Space on your Hard Drive
      • Create a Brain Mask
      • Left-Right Flip Lateral Ventricle Mask
      • Nudging
        • Rotation
      • Jaccard
      • Image Math
    • Other
      • Edit Image Header (Mango)
      • Visualization of Lesions using Maximum Intensity Projection
      • Convert Images from SPM MNI to FSL MNI
  • Resting State
    • Introduction
      • FSL fMRI Resting State Seed-based Connectivity
        • Unix Primer
        • Goals
        • Data
        • Create Mask of Seed Region
        • Extract Time Series from Seed Region
        • Run the FSL FEAT First-level Analysis
        • The FSL FEAT Higher-level Analysis
  • Stroke Lesions
    • Creating a Lesion Mask
      • iPad Drawing Tools
      • Related Pages
        • ITK-SNAP Segmentation of Stroke-related Lesions
        • SPM12 Revised Normalization
        • Image Processing Tips and Tricks
    • Working with Clinical Data
      • Simple Image Fusion
      • CT Scans
        • Gantry Tilt
        • CT Windowing (Contrast) Issues
        • Film ➜ JPEG ➜ NIFTI
    • Lesion Normalization
      • ANTS
        • Data
        • Steps
      • FSL Lesion Normalization
        • Data
        • The 3 Scripts
        • The Originals
      • SPM Lesion Normalization
        • Data
        • Steps
      • SPM Lesion Normalization with Tissue Probability Maps
        • Data
        • Steps
      • SPM Lesion Normalization with Source Weighting Image
        • Data
        • Steps
      • SPM12 Revised Normalization
        • Data
        • Steps
      • Exploratory Comparisons as Tableau Dashboards
        • Brain Mask Matching Dashboard
        • Lesion Preservation Dashboard
      • Overview of Results
      • Recommended Approach
      • Normalization Methods Compared
        • ANTS
        • FSL
        • SPM
  • TMS
    • Introduction
    • Hardware
      • MagPro
      • MEP
    • TMS-Navigator Interface
    • Once per Project: Folders and MNI Planning
    • Flowcharts
      • Before Participant Arrives
      • After Participant Arrives
    • Spike2 Setup (MEP computer)
      • New Data Document
      • Apply Resource File
      • TMS-EMG Configuration
    • Set up Session (Localite computer, Toolbar)
      • Load Anatomical Image: Option 1 DICOMS
      • Load Anatomical Image: Option 2 NIFTI
      • Enter Patient Demographics
      • Surface Threshold
    • Patient Registration Landmark Setup (Toolbar)
    • Brain Segmentation (Toolbar)
      • Brightness and Contrast (Lower Control Area)
      • Peel surface (Lower Control Area)
    • Define Talairach (Menu)
    • Load MNI Planning Targets
    • Rotation and Entry for each Target
      • The Hand Knob
    • Set up Participant
      • Electrodes
      • Resume Patient Registration
        • Acquire Landmarks
        • Surface Registration
    • Coil Calibration
    • Check Camera (Polaris Spectra P7) Position (Toolbar)
    • Set up to Find Motor Hotspot
      • Stimulation (Lower Control Area)
      • Choose Entry/Target (Lower Control Area)
      • Set up Navigation (Lower Control Area)
      • Stimulator
      • MagPro Settings
    • The Motor Hotspot
      • Start Sampling with Spike 2
        • Adjust the Y-axis (Spike 2)
      • Locate the Motor Hotspot
      • Pest
      • Test Threshold for 3/6
      • Spike2: Quit and Stop (Do NOT close)
    • TBS (Theta Burst Stimulation)
    • Wrap Up the Session
      • Save Data
      • Turn off Hardware

Neuroimaging Software

  • ANTS
    • Data
    • Steps
      • The script
      • Alternative approaches
  • FSL
    • FSL Lesion Normalization
      • Data
      • The 3 Scripts
        • Why Skull Strip with optiBET?
      • The Originals
    • FSL fMRI Resting State Seed-based Connectivity
      • Unix Primer
      • Goals
      • Data
      • Create Mask of Seed Region
      • Extract Time Series from Seed Region
      • Run the FSL FEAT First-level Analysis
      • The FSL FEAT Higher-level Analysis
        • Select Each Individual Subject FEAT Analysis
        • Name an Output Directory
        • Run the Higher-level Analysis
    • Image Processing Tips and Tricks
      • Anatomical Image Preparation
        • Prepare T1w Image
        • fslreorient2std
        • Crop Neck with robustfov
        • Correct Extreme Anisotropy
        • Reslice Other Anatomicals into One Space
      • Masks
        • Erode
        • Dilate
        • Fill Holes
        • Cluster Count
        • Cluster Clean
        • Smooth
        • Left-Right Flip and Nudge
      • Check for Hidden Problems
        • fslinfo and fslhd
        • Ensure Zeros, not NaNs
        • Ensure SFORM and QFORM Match
        • Ensure Standard Orientation in NIFTI Header
        • Save Space on your Hard Drive
        • Create a Brain Mask
        • Left-Right Flip Lateral Ventricle Mask
        • Nudging
        • Jaccard
        • Image Math
      • Other
        • Edit Image Header (Mango)
        • Visualization of Lesions using Maximum Intensity Projection
        • Convert Images from SPM MNI to FSL MNI
  • ITK-SNAP
    • ITK-SNAP Segmentation of Stroke-related Lesions
      • Introduction
        • What is a Stroke-related Lesion?
        • What is a Lesion Mask?
        • Why Create a Lesion Mask?
      • Goals
      • Data
      • Setup
      • Select a Region of Interest for Automatic Segmentation
      • Segment the Lesion
        • Thresholding to Isolate the Lesion
        • An Alternative: Clustering to Isolate the Lesion
        • Set Segmentation Labels
        • Place Bubbles
        • Run Active Contour Segmentation
        • Save Workspace
      • Editing the Segmentation
    • Introduction
    • Load and View the Image / Images
    • Understanding Labels
      • Label editor
      • Segmentation labels
    • 2D Segmentation Editing
      • Paintbrush
      • Adaptive Brush
      • Polygon
    • 3D Segmentation Editing
      • Scalpel
    • Add a Second Segmentation
    • View Volume Statistics
  • Mango
    • iMango
    • Edit a NIFTI header
    • Create a NIFTI viewer Webpage
      • Why an HTML NIFTI Viewer is Useful
      • How to Make an HTML NIFTI viewer
  • SPM
    • SPM Lesion Normalization
      • Data
      • Steps
        • Segment: Estimate Warp Field
        • Normalise: Apply Warp Field to Lesion Mask
        • Normalise: Apply Warp Field to Anatomical Image
        • Run Batch and View Results
    • SPM Lesion Normalization with Tissue Probability Maps
      • Data
      • Steps
        • Coregister: Reslice Lesion Mask to TPM Space
        • Segment: Estimate Warp Field
        • Normalise: Apply the Warp Field to Lesion Mask
        • Normalise: Apply Warp Field to Brain and Head
        • Run Batch and View Results
    • SPM Lesion Normalization with Source Weighting Image
      • Data
      • Steps
        • Create Inverse Lesion Mask
        • Old Normalize: Estimate and Write Lesion Mask
        • Old Normalize: Write Anatomy file
        • Run Batch and View Results
    • SPM12 Revised Normalization
      • Data
      • Steps
        • Segment: Estimate Warp Field
        • Normalise: Apply Warp Field to Bias Corrected Head
        • Run Batch and View Results
    • Batch and Scripting

Unix

  • Learn Unix Online with Jupyter lab
    • Three Commands to Rule them All
      • Flags and Arguments: Examples with ls
    • Get Help
    • Directories, Links and Files
      • Directories
    • Summary of Main Points
    • What’s in that File?
      • Summary of Main Points
    • Permissions
      • Summary of Main Points
    • Standard Unix Directory Structure
      • Important Directories
      • The Path
      • Absolute and Relative Paths
    • Actions: cp, mv, rm and wildcards
      • Rename a Directory
      • Learn about Wildcards
      • Learn about remove rm
      • Permissions Again
      • Summary of Main Points
    • Glossary of Commands
    • Other Unix Resources
  • More Unix: Install Neuroimaging Tools
    • Install FSL
    • Set up a Tools Directory
  • HPC for Neuroimaging
    • Useful Links
    • Introduction
    • PROS
    • CONS
    • Tutorial Introduction
    • Sign up for an Account
    • Sign on to OOD
      • The File Explorer and Editor
    • How the HPC differs from your Desktop Computer
      • Storage
      • Jobs: Interactive and Batch Mode
        • Running your First Job
        • Running Lots of Jobs
      • Transferring Files
        • Tiny Files
        • Medium Sized Files
        • Big Files and Directories: Globus
      • Optional Section: Return to a Previous Terminal Session Using Screen
        • Screen Tutorial
      • Deidentifying Data
      • Optional Section: SSH TO HPC
  • Singularity on the HPC
    • Introduction
    • Build Singularity Containers from Dockerhub
    • Build Singularity Containers from Recipes
    • Running a BIDS Singularity container
    • Host OS and Singularity Interactions
    • Building Large Containers
      • Running Out of Space
      • Running Out of Time
    • BIDS Containers
  • Cyverse for Neuroimaging
    • Neuroimaging VM, version 1.1
      • Activating Matlab on Neuroimaging VM
    • General How To and Gotchas
      • Root
      • Bye Bye Home Directory and Modifications
      • Build Your Own
      • Web Desktop Tweaks
      • Terminal font size (on the desktop)
      • Data Transfer
      • Mounting a Volume
      • Detach Volume before deleting the Instance
      • Singularity on Cyverse
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