SpeechLab Toolkit (SLT) v.beta

Reference: [NeuroImage, August 2003]
Region of interest based analysis of functional imaging data, Pages 1303-1316
Alfonso Nieto-Castanon, Satrajit S. Ghosh, Jason A. Tourville and Frank H. Guenther

We are making available a trimmed version of our analysis package. This release includes ASAP (A Segmentation and Parcellation Tool) and RAT2 (ROI Analysis Toolbox for SPM2). RAT2 utilizes matlab objects to create a batch processing environment for SPM2. The same objects are utilized for performing ROI based analyses. The current procedures and their parameters are tuned for our experiments but the flexibility exists to modify them for yours.

Starting with this version, we have moved away from a graphical interface to a script based interface (except ASAP). The reason for this is that a graphical interface can be very easily built using the scriptable interface.

Features:

  • Matlab based
  • Region-of-interest (ROI) based fMRI analyses
  • Integrated with SPM2
  • A simple scriptable batch mode interface to SPM2
  • A user interface for parcellation of cortical regions (A Matlab based CardViews clone)
  • On UNIX platforms, can be used with FreeSurfer for automatic parcellation

Components:
The SLT consists of several different components: some more general than others. The current composition is described in brief below.

  • ROI Analysis Toolbox 2 (RAT2): This is the main component of the package and includes:
    – An SPM2 batch processing system
    – ROI analyses scripts (spm_ROI)
    – Figure creation scripts for both SPM2 and spm_ROI results
    – Preprocessing scripts for ASAP
    – FreeSurfer interaction tools (UNIX only)
  • A Segmentation and Parcellation Program (ASAP): A graphical interface for creating ROI masks for brain images. This tool is a Matlab based clone of the program CardViews.
  • SurfTools: A set of computational geometry tools to work with manifold triangular meshes. In addition it provides the means for including Visualization Toolkit (VTK) functionality in Matlab.
  • FSTools: A set of Matlab scripts provided by the authors of FreeSurfer for accessing and manipulating different FreeSurfer file formats.

[Announcement 31Aug2004] A more recent version has been made available. It is still a work in progress. More updates will be on their way soon. In the meantime, the manual in the SLTdoc folder should get you started. The scripts folder is a bit outdated, but will be updated shortly.

Download SLT v.beta [31Aug2004]
Download the manual: SLTManual.pdf

Platforms:

Technically, this toolbox should work on any platform on which Matlab is supported. However, we have been using it on Linux (Redhat 8.1) and Windows 2000/XP with Matlab 6.5. Therefore, we cannot predict its performance on other configurations.

Licensing and support:

This toolbox utilizes various SPM functions. It is released under the same license as SPM. No formal support or maintenance is provided or implied. We will continue to develop the software to support the needs of our lab.