System Components and Features

SPHARM-MAT is a multifaceted computational analysis tool which allows for the in-depth application of SPHARM expansion techniques to accurately describe the morphometric features of the brain, its various components or other 3D structures. By using a graphical user interface, the toolkit is easy to utilize and allows for enhanced user control in order to specify settings appropriate for each unique study; see Tutorial and Processing Pipeline. Matlab command line scripts are also provided to help users write their own batch scripts; see Command Line and Batch Processing. This chapter organizes relevant information according to the functional components arranged on the GUI.

Parameterization

Relevant chapters

• Spherical Parameterization

Relevant exercises

• Exercise 3.1 Surface Meshes (CALD)
• Exercise 3.2 Voxel Surfaces (CALD)
• Exercise 3.3 Voxel Surfaces (PDM)

Relevant tips

• Parameterization CALD Input and Output
• Parameterization CALD Parameters
• Parameterization PDM Input
• Parameterization PDM Parameters

Expansion

Relevant chapters

• SPHARM Expansion

Relevant exercises

• Exercise 4.1 SPHARM-MAT Expansion
• Exercise 4.2 SPHARM-PDM Expansion

Relevant tips

• SPHARM Expansion Degree
• SPHARM Expansion PDM Difference
• Expand and Align Parameters

Alignment

Relevant chapters

• SPHARM Expansion
• Surface Alignment

Relevant exercises

• Exercise 5.1 FOE Alignment
• Exercise 5.2 SHREC Alignment
• Exercise 5.3 SPHARM-PDM FOE Alignment

Relevant tips

• Alignment FOE Parameters
• Alignment SHREC Parameters
• Expand and Align Parameters

Expand & Align

Relevant chapters

• Surface Alignment

Relevant exercises

• Exercise 4.2 SPHARM-PDM Expansion
• Exercise 5.3 SPHARM-PDM FOE Alignment

Relevant tips

• Expand and Align Parameters

Stat Analysis

Relevant chapters

• Statistical Analysis

Relevant exercises

• Exercise 6.1 T Test
• Exercise 6.2 PCA

Relevant tips

• Stat Analysis T Map Parameters
• Stat Analysis PCA Parameters

Import

Relevant chapters

• Other Utilities

Relevant exercises

• Exercise 7.1 Import

Relevant tips

• Import Parameters

Display Res

Relevant chapters

• Statistical Analysis

Relevant exercises

• Exercise 6.1 T Test
• Exercise 6.2 PCA

Relevant tips

• DisplayRes T-Map Parameters
• DisplayRes PCA Parameters

Utils

FormatConvert

Relevant exercises

• Exercise 2.2: SPHARM-PDM Topology Fix
• Exercise 3.3 Voxel Surfaces (PDM)
• Exercise 4.2 SPHARM-PDM Expansion
• Exercise 5.3 SPHARM-PDM FOE Alignment

Relevant tips

• Format Conversion for Binary Objects
• Format Conversion for Surface Meshes
• Format Conversion for SPHARM Models

TopologyFix

Relevant chapters

• Data Preparation

Relevant exercises

• Exercise 2.1: In-house Topology Fix
• Exercise 2.2: SPHARM-PDM Topology Fix

Relevant tips

• TopologyFix InHouse_Fix Option
• TopologyFix PDM_Fix Option

DisplayObjs

Relevant exercises

• Exercise 2.1: In-house Topology Fix
• Exercise 2.2: SPHARM-PDM Topology Fix
• Exercise 3.1 Surface Meshes (CALD)
• Exercise 3.2 Voxel Surfaces (CALD)
• Exercise 3.3 Voxel Surfaces (PDM)
• Exercise 4.1 SPHARM-MAT Expansion
• Exercise 5.1 FOE Alignment
• Exercise 5.2 SHREC Alignment
• Exercise 5.3 SPHARM-PDM FOE Alignment

Relevant tips

• DisplayObjs Space Option
• DisplayObjs Mesh Option
• DisplayObjs Shade Option
• DisplayObjs Overlay Option
• DisplayObjs Export Option
• DisplayObjs Degree Option
• DisplayObjs Template Option

AverageObjs

Relevant chapters

• Other Utilities

Relevant exercises

• Exercise 7.2 Average Objects

Relevant tips

• AverageObjs Parameters

ScaleObjs

Relevant chapters

• Other Utilities

Relevant exercises

• Exercise 7.3 Scale Objects

Relevant tips

• ScaleObjs Parameters

Tools

• CD - Change directory
• PWD - Show current directory
• Config - Define SPHARM-PDM path for PC and UNIX

Quit

• Quit SPHARM-MAT.