Module Type & Category
Authors, Collaborators & Contact
- Nicole Aucoin: Brigham and Women's Hospital
- Nick Schmansky: MGH
- Doug Greve: MGH
- Contact: Nicole Aucoin, firstname.lastname@example.org
The Qdec Module provides support for the QDEC program from MGH: Query, Design, Estimate, Contrast.
Slicer3 provides integrated file format support for the FreeSurfer geometry files, scalar overlays, and volume files. Through the QdecModule GUI, it also provides an interface to launch queries on subject populations that have been processed by FreeSurfer morphometry autosegmentation pipelines. Users can also load precomputed data sets and inspect the statistical processing results.
Use Cases, Examples
This module is especially appropriate for these use cases:
- Use Case 1: visualising the output of FreeSurfer's GLM processing
- Use Case 2:
Examples of the module in use:
- Example 1: 2007 Project Week page
- Example 2
Links to tutorials explaining how to use this module:
Quick Tour of Features and Use
- Obtained from your local MRI scanner, processed using FreeSurfer
- Place them in a subjects directory on disk
- Add a qdec directory at the same level as the subjects
- Create a qdec.table.dat file to describe the subject
Once you've set up a subjects directory, set your SUBJECTS_DIR environment variable (you'll need to restart Slicer3). In that directory, make sure you've put the fsaverage subject created from the subjects you wish to analyse. When the FreeSurfer analysis is done over a set of subjects, an average subject is computed. The fsaverage directory holds an averaged brain on which the group statistics will be displayed
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).
ID Gender Age CSF OAS1_0001_MR1 F 74 1229.0 OAS1_0002_MR1 F 55 773.0 OAS1_0003_MR1 F 73 1448.0 OAS1_0004_MR1 M 28 1286.0 OAS1_0005_MR1 M 18 1304.0 OAS1_0006_MR1 F 24 909.0
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). Slicer3 uses it's QDEC library to unpack the .qdec file and load the contents:
- Average brain surface file
- Brain curvature overlay
- Statistical overlays corresponding to the contrast questions
- Volume holding data for each subject
Once the results are loaded, the first point in the average brain is used to pop up a plot of all the subject values at that vertex. You can plot results at various vertices by setting the setting the 3DViewer mouse mode to 'pick' using the toolbar button and clicking on the brain model. The plot window shows the RAS and index of the chosen vertex.
- Subjects panel:
|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:
- Display panel:
You can inspect all the statistical results of the analysis by switching to different overlays using the “Questions” menu.
Once the average brain surface and statistical overlays are loaded into Slicer3, you can use the QueryAtlas module to load the brain region labels and browse the annotations.
Notes from the Developer(s)
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.
On the Dashboard, these tests verify that the module is working on various platforms:
- QdecContrastTest1 Libs/Qdec/Testing/QdecContrastTest1.cxx
- QdecDataTableTest1 Libs/Qdec/Testing/QdecDataTableTest1.cxx
- QdecFactorTest1 Libs/Qdec/Testing/QdecFactorTest1.cxx
- QdecGlmDesignTest1 Libs/Qdec/Testing/QdecGlmDesignTest1.cxx
- QdecGlmFitResultsTest1 Libs/Qdec/Testing/QdecGlmFitResultsTest1.cxx
- QdecGlmFitTest1 Libs/Qdec/Testing/QdecGlmFitTest1.cxx
- QdecProjectTest1 Libs/Qdec/Testing/QdecProjectTest1.cxx
- QdecSubjectTest1 Libs/Qdec/Testing/QdecSubjectTest1.cxx
- QdecUtilitiesTest1 Libs/Qdec/Testing/QdecUtilitiesTest1.cxx
- QdecModuleLibs Modules/QdecModule/Testing/QdecModuleLibs.tcl
Follow this link to the Slicer3 bug tracker.
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
Module Doxygen documentation:
Library Doxygen documentation:
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.