This directory contains a release of the University of Michigan Psychiatry 
Neuroimaging Methods Core tools.  The version number of the release can be
found in ./.local/mc_releasetag

For help with these tools contact us at MethodsCoreHelp@umich.edu

The goal of the Neuroimaging Methods core is to provide all investigators in 
the Department of Psychiatry -- especially junior faculty and young 
investigators -- with the latest and best in neuroimaging analysis tools.

The Core consists of Robert Welsh and Chandra Sripada (Co-directors)
as well as Mike Angstadt and Daniel Kessler (Research Computer
Specialists).  An Executive Committee consisting of PIs from the
department sets the Core's agenda and oversees activities.

Our goal is to make sure Methods Core tools are:
    *User-friendly including extensive commenting and informative error 
    messages.
    
    *Integrated and consistent across tools.
    
    *Fast, using a variety of methods to reduce disk operations and accelerate
    performance.
    
    *Well documented including help files and, in many cases, practical video 
    documentation.
    
    *Supported by Methods Core personnel at MethodsCoreHelp@umich.edu
    
    *Frequently updated to work with current versions of SPM, FSL, MarsBar, etc.


Please give us your feedback about how we're doing.


Release Notes:
2/20/2017  - Release 3.0
	     This release updates Methods Core to SPM12 (R7219)
	     This includes the addition of a Preprocess folder which contains
	     MATLAB based preprocessing template/central scripts.
	     The ConnTool folder also now contains AnatomyErode scripts to aid
	     in creating eroded WM/CSF masks for resting state processing.
	     
5/3/2016   - Release 2.0
	     This release incorporates many substantial updates & improvements to
	     previously released tools, including
	     - ConnTool
	     - ExtractionsScript
	     - FirstLevel
	     - GraphTheory
	     - PPI
	     - QualityChecks
	     - SecondLevel
	     - spm8Batch
	     - svmbatch
	     - core (core functionality & SPM releases)

3/28/2014  - Release 1.9
	     This release adds the GraphTheory toolbox to perform graph theoretic analyses on connectome data.

2/7/2014   - Release 1.8
	     This release adds enhancements to ConnTool, including the ability to perform ALFF and fALFF analyses.

11/20/2013 - Release 1.7
	     This release adds an advanced tool (svmbatch) to support Paired SVM Analyses.

10/1/2013  - Release 1.6
             This release adds a tool (ConnTool) to support Connectivity Analyses.

5/8/2013   - Release 1.5
             This release adds tools to support both standard and generalized
             PPI. These scripts can be found in the PPI directory.
             They include batched and automated VOI extration, automated
             generation of PPI regressors for multiple ROIs, and modifications
             to FirstLevel template script for easier loading of multiple
             subject-specific regressor files at the first level.

4/8/2013   - Release 1.4
             This release adds scripts for quality checking during preprocessing.
             These can be found in the QualityChecks folder.
             Minor revisions were made to spm8Batch including the ability to use 
             SPMs New Segment instead of VBM, as well as extracting principle 
             components from white matter and CSF segments.

2/13/2013  - Release 1.3
             This release adds scripts to extract betas from SPM designs in the
             ROIScripts folder.
             The Methods Core repository now also includes the latest distribution
             of Marsbar in Utilities/marsbar/marsbar-0.43
             Includes a few minor FirstLevel bug fixes
             
10/2/2012  - Release 1.2
             This release adds matlab scripts to perform second level analysis
             in SPM.

9/5/2012   - Release 1.1 
	     This release adds a suite of matlab-driven
	     scripts to support first level analysis.

8/1/2012   - Release 1.0 
	     First public release of MethodsCore tools.  This release contains a 
	     suite of command-line scripts to preprocess fMRI data as well as 
	     perform several basic data quality checks.