Modules:QDECModule-Documentation-3.4

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QDEC

QDEC

QDEC GUI and inflated brain

QDEC Plot window

General Information

Module Type & Category

Type: Interactive

Category: Informatics

Authors, Collaborators & Contact

• Nicole Aucoin: Brigham and Women's Hospital
• Nick Schmansky: MGH
• Doug Greve: MGH
• Contact: Nicole Aucoin, nicole@bwh.harvard.edu

Module Description

The Qdec Module provides support for the QDEC program from MGH: Query, Design, Estimate, Contrast.

Usage

Examples, Use Cases & Tutorials

• This module is useful for visualising the output of FreeSurfer's GLM processing
• 2007 Project Week page
• Presentation from 2007

Quick Tour of Features and Use

Before you start: Set up a subjects directory and set your SUBJECTS_DIR environment variable (you'll need to restart Slicer3). In that directory, put the set of subjects you wish to analyse, along with the fsaverage subject. Then make a subdirectory qdec, and in it place your qdec.table.dat file along with any .level files describing the discrete factors (ie gender.levels will have 'male' and 'female' on two separate lines).

You can also load precomputed .qdec archives using the 'Load Results Data File' button. This requires unzip and rm, and you can point Slicer to these applications via the Application Settings interface (View->Application Settings).

Once the results are loaded, you can plot results at various vertices by setting the setting the 3DViewer mouse mode to 'pick' using the toolbar button.

• Subjects panel:

	Set SUBJECTS_DIR
	Load Table Data File
	Load Results Data File
	Table of Subjects

• Design panel:
• Display panel:

Development

Dependencies

The QDEC library (included with Slicer3) is required for this module. FreeSurfer is required for this module's use in calculating new GLM results, but is not necessary for loading pre computed ones.

Known bugs

Follow this link to the Slicer3 bug tracker.

Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

Source code & documentation

Module Source Code:

• vtkQdecModuleGUI.cxx, vtkQdecModuleGUI.h
• vtkQdecModuleLogic.cxx, vtkQdecModuleLogic.h
• vtkGDFReader.cxx, vtkGDFReader.h

Library Source Code:

• QdecContrast.cpp, QdecContrast.h
• QdecDataTable.cpp, QdecDataTable.h
• QdecFactor.cpp, QdecFactor.h
• QdecGlmDesign.cpp, QdecGlmDesign.h
• QdecGlmFit.cpp, QdecGlmFit.h
• QdecGlmFitResults.cpp, QdecGlmFitResults.h
• QdecProject.cpp, QdecProject.h
• QdecSubject.cpp, QdecSubject.h
• QdecUtilities.cpp, QdecUtilities.h
• vtkFreeSurferReaders.tcl

Module Doxygen documentation:

• GUI
• Logic
• GDF Reader

Library Doxygen documentation:

• GLM Design
• GLM Fit
• Factor
• Data Table
• Contrast
• GLM Fit Results
• Project
• Subject
• Utilities

More Information

Acknowledgment

This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.