Difference between revisions of "Modules:QDECModule-Documentation-3.4"

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== Development ==
 
== Development ==

Revision as of 21:25, 25 February 2009

Home < Modules:QDECModule-Documentation-3.4

Return to Slicer 3.4 Documentation

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

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:
SlicerQDECSubjects-3.4.jpg
Set SUBJECTS_DIR Set the SUBJECTS_DIR environment variable
Load Table Data File Load a .dat file
Load Results Data File Load a .qdec file
Table of Subjects Filled in from the subjects on disk
  • Design panel:
SlicerQDECDesign-3.4.jpg
Design Name Pick a name for the design
Discrete Factors Choose up to two discrete factors for the General Linear Model calculation
Continuous Factors Choose two continuous factors for the General Linear Model calculation
Measures Measure Hemisphere Smoothness
Pick from the drop down menu of measures: thickness, sulc, curv, jacobian, area. This must have been calculated on the subject brains, as a scalar overlay file is going to be looked for. Choose the left or right brain hemisphere on which to do the calculations Choose a smoothing factor, full width half maximum, in mm.
Run GLM Fit Find the glm executable from the FreeSurfer installation and run it with the selected factors and measures.
  • Display panel:


SlicerQDECDisplay-3.4.jpg
Question Pick which overlay is represented on the average brain, the overlays are generated in response to the question that was posed by the measures, for example, does the average thickness differ from zero? Selecting a new overlay also resets the colour node used to map the scalars on the model. You can manually select an overlay and color node in the Models Display panel if you wish.

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:

Library Source Code:

Module Doxygen documentation:

Library Doxygen documentation:

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.

References