Resources: Tools and Utilities

Following are some software tools that we think may be useful. Please note that while we attempt to make sure software distributed here works as intended, this code is largely research code for which we do not have the resources to provide technical support.

• BFC Correction tool: This tool allows user guided bias field correction by manually selecting points.

• Matlab utility functions: for processing data generated using BrainSuite and SVReg.This includes functions for smoothing functions on surfaces, ROIwise and pointwise group differences, inverting the volumetric map, regenerating stats file after manual corrections to the label file, labeling of surfaces and volumes based on manually drawn cortical ROIs, computing stats for arbitrary ROIs and creating a new atlas.

• Temporal non-local means (tNLM) filtering: A novel filtering approach which allows direct visualization of the brain activity in real-time using functional MRI.

• BDP Addons: Tools for processing data generated using BrainSuite and BDP. It also includes a general purpose affine registration tool.

• Prepare Fieldmap: A command line tool for converting scanner saved fieldmap to units of radians/sec.

• Cortical Delineation Protocol

• Add sform matrix to NIfTI-1 files: This tool adds sform matrix to NIfTI header, if it is absent.

• Joint Denoising of Diffusion MRI Magnitude Images: This tool implements a penalized maximum likelihood estimation method for reducing noise in diffusion MRI magnitude images.

• BrainSuite Sample Dataset: Mirror of sample dataset for BrainSuite training.

• Eigen file (.eig) to NIfTI converter: Matlab script to converts .eig.nii.gz files saved by BrainSuite Diffusion Pipeline (BDP) to standard NIfTI-1 format.

• TractConnect: Diffusion Fiber Tract Analysis tool for BrainSuite.

• IPEDcorrect: Distortion correction of diffusion weighted MRI images using interlaced q-space sampling

• BrainSync: An orthogonal transformation for synchronization of fMRI data across subjects

• DigiWarp: a method for deformable mouse atlas warping to surface topographic data

• deface_mri: Anonymization tool for brain MRI.

• SVReg_multiparc:A plugin for BrainSuite for generating multiple parcellations