Modules:QDECModule-Documentation-3.6

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Gallery of New Features


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.

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.

Usage

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:

Tutorials

Links to tutorials explaining how to use this module:


Quick Tour of Features and Use

Subject scans

  • 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).

Sample qdec.table.dat:

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

Sample gender.levels:

male
female

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.

SlicerQDECPlot-3.4.jpg

Panels

  • 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 On machines that have a FreeSurfer binary installation, you can use Slicer3 to set up queries and launch the mri_glmfit executable with the selected factors and measures. Slicer3 will automatically load the processing results for inspection.
  • Display panel:

You can inspect all the statistical results of the analysis by switching to different overlays using the “Questions” menu.

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.

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.

Development

Notes from the Developer(s)

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.

Tests

On the Dashboard, these tests verify that the module is working on various platforms:

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