Applied Neurobiological Imaging

Data Processing Archives

Preprocessing

• View Data
  • Load Data in BrainSuite and Shapeviewer
• Overview of Steps needed to Preprocess data.
  • Step by Step Protocol on how to process structural MRI data.
    • Download data from Brain Mapping Center
    • Converting Dicom data
    • Run Freesurfer on Data using the LONI Pipeline
    • Convert Freesurfer surfaces to Object format
    • Sulcal line drawing
    • Sulcal line drawing in Shapeviewer
    • Combine sulcal lines to single ucf file
    • Elastic Surface Warping (Cortical Pattern Matching)
    • Convert Warping Surface Outputs to .ucf
    • Convert Freesurfer images (.mgz) to anaylze and create Dist Q files
• Useful Processing Protocols
  • Averaging analyze images
• Masking and Skull Stripping
  • Masking Protocol (using the MNI Display program)
  • Skull Stripping in MultiTracer Using the TraceWalker Utility
  • Converting an analyze file to a mask using BrainSuite
  • Hemisphere Masking in Display
  • Hemisphere Masking in BrainSuite
• Tracing Subcortical Structures in MultiTracer
  • Hippocampus tracing protocol (or download hippo_protocol.doc file)
• Shape Analysis Preprocessing (Surface Deformation Scripts)
• Object creation
• DTI-Related Protocols
  • DTI Processing in DTI Studio
  • Load DTIStudio Tractography Files in DTIStudio
  • Fiber Tracking
    • Identifying the arcuate fasciculus in DTIStudio using a multiple ROI approach.
    • Identifying the cingulate gyrus component of the cingulum in DTIStudio using a multiple ROI approach.
    • Identifying the fornix in DTIStudio using a multiple ROI approach.
    • Identifying the inferior longitudinal fasciculus in DTIStudio using a multiple ROI approach.
    • Identifying the inferior occipitofrontal fasciculus in DTIStudio using a multiple ROI approach.
    • Identifying the uncinate fasciculus in DTIStudio using a multiple ROI approach.
• fMRI Protocols
  • View fMRI data in BrainSuite

Tensor Based Morphometry (TBM)

• Running TBM Processing and Analysis through the LONI Pipeline.
  • TBM Atlas Generation
  • TBM Jacobian Generation
  • TBM Statistical Analysis (Volume Regression Analysis)
  • TBM Longitudinal Jacobians and Analysis (One Sample T-Test)

Statistical Analysis

• Using R statistical analysis software (http://www.r-project.org)
  • Creating p maps using R (using an ANOVA)
  • Mixed Model: Creating p maps using R but modeling for random factors (using an ANOVA)
  • Running permutations in R with an ROI mask
  • Finding mean cortical thickness values using R
  • Running False Discovery Rate (FDR) Correction using R
  • Creating UCF Regions of Interest (ROIs)
• Using SPM5
  • Voxel Based Morphometry Analysis of DTI Data Using the General Linear Model
  • Voxel Based Morphometry Analysis of DTI Data Using T-Tests

Creating Figures from DTI Data

• Working with DTI Data in BrainSuite 2.45
  • Creating objects from masks: Use ROI masks to create 3D overlays on DTI data.
  • Adding Objects to *rgb Data: Adding the 3D objects to your figures showing your DTI colormap data.
  • Glyphs: Show tensor directional information with glyphs in BrainSuite.

Pipeline Modules

• Pipelines from our group available for download
• Running FEAT in the LONI Pipeline

Preparing Figures for Publications and Presentations

• Creating 3D Object Art
  • This protocol describes how to display 3D cortical objects with different cut-out views to show subcortical structures or activation at a particular slice (for fMRI).
• Loading and viewing UCFs with ShapeViewer

Miscellaneous

• Cortical Thickness (Flat-Mapping) Scripts (Under Construction)
• Simple UNIX Tutorial (foreach loops, etc.)

Other Protocols

• LONI Resource Protocols
• Surface Curve Protocol (from Dr. Elizabeth Sowell's lab)
• Medial Lines Protocol (from Dr. Elizabeth Sowell's lab)
• Cortical Surface Analyses, Making Meshes, Working with UCFs (from Dr. Paul Thompson's lab)

Software Used By Our Group

See the BMAP Software page for more information on software created in the lab.

• Automated Image Registration (AIR)
• ShapeViewer
• MultiTracer
• ShapeTools

Useful Links (external)

• Tutorials
  • An Intro to SPM
  • Automated Image Registration (AIR)
  • Managing Memory in MATLAB
  • MultiTracer Help
  • Overlaying Functional Activation on 3D Cortex Models
  • Psychophysics Toolbox (MATLAB)
• Support
  • FSL
  • MedINRIA software for DTI Tractography and fMRI analysis
  • SPM Email List