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Methods Core is pleased to announce the release of Methods Core Release 1.6. This release makes available the locally developed Connectivity ToolBox (called ConnTool). This tool was mainly developed by Robert Welsh over the past number of years and has been folded into Methods Core with contributions by Methods Core members. 

The tool is inherently batch and follows quite closely similar structure to FirstLevel templates.

The tool can be found in your local MethodsCore directory under ConnTool

There is extensive documentation to be found in (along with other documents):

ConnTool/Documentation/ConnTool_HowTo.pdf (or click here)

The main template script you will be copying to modify for your local analysis is called:


This template is fully described in the documentation. The tool has been extensively tested inside and outside of MethodsCore, however, we do appreciate feedback in usage and errors. Please remember to direct your questions to

The tool is a seed based connectivity tool. It allows for creation of either correlation/z images or correlation/z maps. The tool has a wide range of flexibility for preprocessing of the data prior to correlation analysis. This processing includes all of the following as options:
  • Detrending
  • Motion Regression
  • CSF PCA Regression, ala COMPCOR
  • WM PCA Regression, ala COMPCOR
  • Global Signal Regression
  • Spike Artifact Replacement via smoothed interpolation (this is a time consuming step)
  • FFT Bandpass filtering (with slight roll-off of edges)
  • Spike Artifact Removal (Editing/Scrubbing)

The code is flexible and allows you to specify the order of the preprocessing as your scientific question may dictate.

We are pleased to announce the new features fALFF and ALFF as part of the Methods Core distribution of ConnTool.

You do the processing like normal with changes in some of the input parameters. The output is either fALFF or ALFF images, you treat these as you would a z-image or a contrast image and enter into a 2nd level analysis.

In the template script "ConnTool_batch_mc_template.m" there is a new section for defining the one or two different frequency bands. For ALFF you need one frequency band, for fALFF you need two. For fALFF your first frequency band MUST be contained inside your 2nd frequency band. Additionally you should NOT include a frequency of 0 (zero). In the output section you will indicate whether you want "falff" or "alff" images. Please be sure to read the documentation thoroughly in the ConnTool/Documentation directory, it has been updated to reflect this new functionality.

For literature behind these calculations please refer to :