Functional Map Viewer and Analysis Tools

This MATLAB-based toolkit provides functionality for viewing, analyzing, and comparing different functional maps, particularly focused on motion processing areas and visual cortex analysis.

Main Components

The toolkit consists of three main components:

1. Run Analysis (run_all.m): Data processing and analysis pipeline
2. Statistical Analysis (run_stats.m): Statistical testing and group analysis
3. View Maps (view_fv): Visualization tool for functional maps

1. Run Analysis (run_all.m)

The run_all.m script handles the main data processing pipeline, including:

• Loading and preprocessing fMRI data
• Computing beta weights for different conditions
• Processing task-specific data (motion, hand, transparent motion, etc.)
• Saving results in MGZ format

Key Features

• Supports multiple task types (motion, hand, transparent motion, etc.)
• Handles design matrix creation and HRF convolution
• Processes noise regressors and motion parameters
• Saves results in FreeSurfer-compatible format

2. Statistical Analysis (run_stats.m)

The run_stats.m script performs statistical analysis across subjects, including:

• Group-level statistical testing
• Comparison of different conditions
• Visualization of statistical results
• Analysis of hemispheric differences

Features

• Supports multiple statistical tests (t-tests, correlations)
• Handles both individual subject and group-level analysis
• Provides visualization tools for statistical results
• Supports analysis of different ROIs and conditions

3. View Maps (view_fv)

The main visualization functionality is provided through the view_fv function, which allows visualization and comparison of various functional maps including:

• Motion processing areas (MT+)
• Visual field maps
• Myelin maps
• Population receptive field (pRF) parameters
• Various motion conditions and experimental comparisons

Usage

view_fv(subject, bidsDir, map1, map2, ...)

Parameters

• subject: Subject identifier (e.g., 'sub-0037')
• bidsDir: Path to BIDS-formatted data directory
• map1, map2, ...: Maps to compare/visualize

Example Comparisons

The tool supports various types of comparisons:

1. Motion Conditions:

view_fv(sub, bidsDir, 'out', 'in', 'cw', 'ccw');

2. Visual Field Maps:

view_fv(sub, bidsDir, 'l', 'upper', 'lower', 'prfvista_mov/angle_adj');

3. PRF Parameters:

view_fv(sub, bidsDir, 'angle_adj', 'eccen', 'sigma');

4. Myelin Maps:

view_fv(sub, bidsDir, 'SmoothedMyelinMap_BC', 'mt+2');

Available Maps

The tool supports visualization of various map types:

• Motion processing: 'mt+1', 'mt+2'
• Visual field: 'l', 'upper', 'lower'
• PRF parameters: 'angle_adj', 'eccen', 'sigma'
• Myelin maps: 'SmoothedMyelinMap_BC', 'MyelinMap_BC'
• Motion conditions: 'oppo2', 'oppo3', 'cd1', 'cd2'

Requirements

• MATLAB
• FreeSurfer
• BIDS-formatted data directory
• Required MATLAB toolboxes:
  • GLMdenoise
  • nsdcode
  • vistasoft
  • cvncode
  • knkutils
  • gifti
  • GLMsingle

Data Organization

The tool expects data to be organized in a BIDS-compatible directory structure. The base directory should be specified in the bidsDir parameter.

Notes

• The tool supports comparison of different experimental runs and conditions
• Multiple maps can be compared simultaneously
• Custom combinations of maps can be created based on research needs
• Statistical analysis can be performed at both individual and group levels