Table of Contents

Welcome!

Over the years we have developed a number of tools to process and visualize neuroimaging data for the Harvard Aging Brain Study. As much as possible we like to make our tools publicly available, both to aid in the transparency and reproducibility of our research, and to aid other researchers.

Hopefully some of you out there will find some of this useful and it will save you some time and hassle.

For a more interactive forum, please join the google groups at: https://groups.google.com/forum/#!forum/fmri_matlab_tools or post to the SPM list with the term “MR Tools help” in the subject line.

This new page is replacing the former wiki mrtools.mgh.harvard.edu. Pages form the old wiki will now redirect to this page.

NOTE: Each section on this page contains a link in the section header that will take you to a page with additional information.

Enjoy!

Aaron P. Schultz and the Harvard Aging Brain team.

GLM Flex Fast2

GLM_Flex_Fast2 is an alternate version of GLM_Flex that focuses on processing speed and ease of model specification.

We recommend using this version of the GLM_Flex code, and are planning to make this branch the primary focus of continued development.

SurfPlot

surfPlot is a tool for making quick and pretty surface renderings from MNI space. This function uses the FSaverage brain from Freesurfer, and uses the standard mapping from voxel space to vertex space. Importantly this tool only works if your data is in MNI space, it cannot be used to map native space to native […]

SchemaBall

Simple Circos style plotting for MATLAB.

This script is an adaptation from two recent contributions.

fcMRI Processing Tools

This package contains my batch scripts based on SPM8 for preprocessing fMRI data for functional connectivity analysis, as well as assorted tools for making seed maps, regional homogeneity maps, hub maps, and extracting time-courses from data

Task fMRI Processing Tools

Similar to the fcMRI preprocessing tools, this package is focused on task based fMRI. The package includes both preprocessing and first level analysis scripts, again based around SPM8.

TBR (Template Based Rotation)

Template Based Rotation (TBR) is new method for creating functional connectivity maps based on prior whole brain parcellations.

Our MNI template space version the GTMseg atlas can be downloaded here.

Downloads

I’ve made both individual packages and a master package. For the May-2014 update I recommend downloading the full package. Note: Full package, GLM_Flex, Visualization Tools, and Utilities were updated on May 26th, 2014. Other packages were last updated on May 13th 2014. Note: Found and fixed a few more bugs. GLM_Flex, Visualization Tools, and Utilities […]