Difference between revisions of "Modules:QDECModule-Documentation-3.4"
Line 46: | Line 46: | ||
| rowspan="5"| [[Image:SlicerQDECSubjects-3.4.jpg]] | | rowspan="5"| [[Image:SlicerQDECSubjects-3.4.jpg]] | ||
|- | |- | ||
− | | Set SUBJECTS_DIR | + | | Set SUBJECTS_DIR |
+ | | set the SUBJECTS_DIR environment variable | ||
|- | |- | ||
− | | Load Table Data File | + | | Load Table Data File |
+ | | Load a .dat file | ||
|- | |- | ||
− | | Load Results Data File | + | | Load Results Data File |
+ | | Load a .qdec file | ||
|- | |- | ||
− | | Table of Subjects | + | | Table of Subjects |
+ | | Filled in from the subjects on disk | ||
|} | |} | ||
* '''Design panel:''' | * '''Design panel:''' | ||
+ | {| border="1" | ||
+ | |- | ||
+ | | rowspan="8"| [[Image: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 | ||
+ | |- | ||
+ | | rowspan="2"| 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:''' | * '''Display panel:''' | ||
Revision as of 21:21, 25 February 2009
Home < Modules:QDECModule-Documentation-3.4Return to Slicer 3.4 Documentation
QDEC
QDEC
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 | 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:
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:
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.