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I work for MGH at the Martinos Center in Charlestown, MA. I am a data analyst and programmer for Dr. Reisa Sperling and the Harvard Aging Brain Study (Visit the HABS website here), focusing on memory, aging and Alzheimer’s.
I do a lot of data analysis and scripting in matlab, so I decided to put together this web site to share some of my matlab scripts. 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. I have a filter in place that will notify me of SPM threads with that tag in the subject line.
This wiki is replacing the website at http://nmr.mgh.harvard.edu/harvardagingbrain/People/AaronSchultz/Aarons_Scripts.html. Pages on that site will now begin redirecting to this wiki.
NOTE: Each section on this page contains a link in the section header that will take you to a page with additional information.
Aaron P. Schultz
NOTE: The original GLM_Flex tool has not been updated to GLM_Flex2. The new version includes a fix that ensures that the results are always computed on a type III sums of squares.
GLM Flex is a set of second level neuroimaging analysis tools that serves as an alternative to the stock SPM8 utilities.
GLM Flex is written for MATLAB, and requires and SPM8 installation.
GLM Flex was designed to be a general purpose second level SPM tools with some additional features over what is available in SPM8:
1. GLM Flex uses partitioned error terms. 2. GLM Flex can analyze voxels with missing data. 3. GLM Flex can be used to automatically remove outliers. 4. GLM Flex can be used to run analyses with more factors than SPM8 will allow. 5. GLM Flex can be used to run second level models on FreeSurfer surface volumes (requires a freesurfer install).
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.
FIVE (Functional Image Visualization Environment)
FIVE is a MATLAB tool for viewing 3D image data. The main focus of this tool is on visualizing statistical parametric maps (SPMs) overlaid on a standard brain (i.e. the MNI-152 template), though other options for native space results are also available.
FIVE was designed to allow for quick review of SPMs with various threshold options, peak detection (via peak_nii), plotting results from specific regions/clusters/spheres/voxels, and for creating images of SPM for inclusion in papers, presentations, etc...
Follow the link above for more detailed information.
This is a handy new script that I put together for creating quick surface renderings of volumetric data. This script currently only works with data in normalized group space (MNI152 or MNI305). The function uses a static mapping from MNI space to FSaverage from Freesurfer. I've bundled in some mat file so that this will work without need an FS installation, and have set this up as both a stand-alone tool and an option from within FIVE. Follow the link for more information.
Simple Circos style plotting for MATLAB.
This script is an adaptation from two recent contributions.
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.
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.
The TBR papers was accepted at Neuroimage. The paper can be found here: http://authors.elsevier.com/a/1Pffz3lc~qos5z
Information about various helpful utility functions.
TBR algorithm and templates are now live!
August 21st 2015 - I have updated all scripts on the download page to the current versions that I am using.
Notable changes include: Compatibility with SPM12 and MATLAB 8+; GLM_Flex_Fast4 which includes the ability to perform variance covariance correction is now part of the package; changes to the surface rendering scripts with an option for a partially inflated brain (a la carret), as well as new default shading schemes for surface underlays; GLM_Flex has been removed from the package and GLM_Flex_Fast is now the only option for the GLM package.
May 26th 2014, small updates / bug fixes for GLM_Flex, Utilities, and Visualizations. FIVE now has more color mapping options based on brewer colors, and has an option for specifying custom colors.
Script update for May 2014. Bug fixes, new plotting tools, updates to GLM_Flex_Fast2 and more...
This wiki is replacing the website http://nmr.mgh.harvard.edu/harvardagingbrain/People/AaronSchultz/Aarons_Scripts.html . Please replace your bookmarks and links to point towards this wiki.
For historical details please follow the link.