Nicole at 22:57, 26 March 2010

2010-03-26T22:57:19Z

Nicole: /* Usage */

2010-03-26T22:56:40Z

Usage

Nicole: /* Tests */

2010-03-26T22:55:02Z

Tests

Nicole: Created page with 'NOTOC ===QDEC=== QDEC {| |QDEC GUI and inflated brain |QDEC Plot window |} == Gener…'

2010-03-26T22:54:45Z

Created page with '__NOTOC__ ===QDEC=== QDEC {| |thumb|280px|QDEC GUI and inflated brain |thumb|280px|QDEC Plot window |} == Gener…'

New page

__NOTOC__
===QDEC===
QDEC

{|
|[[Image:SlicerQDECGUI-3.4.jpg|thumb|280px|QDEC GUI and inflated brain]]
|[[Image:SlicerQDECPlot-3.4.jpg|thumb|280px|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 ==

===Examples, Use Cases & Tutorials===

* This module is useful for visualising the output of FreeSurfer's GLM processing
*[http://www.na-mic.org/Wiki/index.php/Projects/Slicer3/2007_Project_Week_QDEC_Slicer3_Integration 2007 Project Week page]
*[http://wiki.na-mic.org/Wiki/index.php/Image:Slicer3QDEC_AHM2007.ppt Presentation from 2007]

===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:
<pre>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</pre>

Sample gender.levels:
<pre>male
female</pre>

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.

[[Image:SlicerQDECPlot-3.4.jpg]]

====Panels====

* '''Subjects panel:'''

{| border="1"
|-
| rowspan="5"| [[Image: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:'''
{| 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
| 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.

{| border="1"
|-
| rowspan="2"| [[Image: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 [http://wiki.slicer.org/slicerWiki/index.php?title=Modules:QueryAtlas-Documentation-3.4 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 [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* QdecContrastTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/Testing/QdecContrastTest1.cxx Libs/Qdec/Testing/QdecContrastTest1.cxx]
* QdecDataTableTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/Testing/QdecDataTableTest1.cxx Libs/Qdec/Testing/QdecDataTableTest1.cxx]
* QdecFactorTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/Testing/QdecFactorTest1.cxx Libs/Qdec/Testing/QdecFactorTest1.cxx]
* QdecGlmDesignTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/Testing/QdecGlmDesignTest1.cxx Libs/Qdec/Testing/QdecGlmDesignTest1.cxx]
* QdecGlmFitResultsTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/Testing/QdecGlmFitResultsTest1.cxx Libs/Qdec/Testing/QdecGlmFitResultsTest1.cxx]
* QdecGlmFitTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/Testing/QdecGlmFitTest1.cxx Libs/Qdec/Testing/QdecGlmFitTest1.cxx]
* QdecProjectTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/Testing/QdecProjectTest1.cxx Libs/Qdec/Testing/QdecProjectTest1.cxx]
* QdecSubjectTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/Testing/QdecSubjectTest1.cxx Libs/Qdec/Testing/QdecSubjectTest1.cxx]
* QdecUtilitiesTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/Testing/QdecUtilitiesTest1.cxx Libs/Qdec/Testing/QdecUtilitiesTest1.cxx]
* QdecModuleLibs [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/QdecModule/Testing/QdecModuleLibs.tcl Modules/QdecModule/Testing/QdecModuleLibs.tcl]

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Module Source Code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/QdecModule/vtkQdecModuleGUI.cxx vtkQdecModuleGUI.cxx], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/QdecModule/vtkQdecModuleGUI.h vtkQdecModuleGUI.h]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/QdecModule/vtkQdecModuleLogic.cxx vtkQdecModuleLogic.cxx], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/QdecModule/vtkQdecModuleLogic.h vtkQdecModuleLogic.h]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/QdecModule/vtkGDFReader.cxx vtkGDFReader.cxx], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/QdecModule/vtkGDFReader.h vtkGDFReader.h]

Library Source Code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/QdecContrast.cpp QdecContrast.cpp], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/QdecContrast.h QdecContrast.h]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/QdecDataTable.cpp QdecDataTable.cpp], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/QdecDataTable.h QdecDataTable.h]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/QdecFactor.cpp QdecFactor.cpp], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/QdecFactor.h QdecFactor.h]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/QdecGlmDesign.cpp QdecGlmDesign.cpp], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/QdecGlmDesign.h QdecGlmDesign.h]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/QdecGlmFit.cpp QdecGlmFit.cpp], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/QdecGlmFit.h QdecGlmFit.h]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/QdecGlmFitResults.cpp QdecGlmFitResults.cpp], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/QdecGlmFitResults.h QdecGlmFitResults.h]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/QdecProject.cpp QdecProject.cpp], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/QdecProject.h QdecProject.h]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/QdecSubject.cpp QdecSubject.cpp], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/QdecSubject.h QdecSubject.h]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/QdecUtilities.cpp QdecUtilities.cpp], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/QdecUtilities.h QdecUtilities.h]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/vtkFreeSurferReaders.tcl vtkFreeSurferReaders.tcl]

Module Doxygen documentation:

*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkQdecModuleGUI.html GUI]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkQdecModuleLogic.html Logic]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkGDFReader.html GDF Reader]

Library Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classQdecGlmDesign.html GLM Design]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classQdecGlmFit.html GLM Fit]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classQdecFactor.html Factor]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classQdecDataTable.html Data Table]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classQdecContrast.html Contrast]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classQdecGlmFitResults.html GLM Fit Results]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classQdecProject.html Project]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classQdecSubject.html Subject]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classQdecUtilities.html 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.

===References===

← Older revision		Revision as of 22:57, 26 March 2010
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 == Usage ==
-===Examples, Use Cases & Tutorials===
+===Use Cases, Examples===
 ===Quick Tour of Features and Use===

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 * QdecUtilitiesTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/Qdec/Testing/QdecUtilitiesTest1.cxx Libs/Qdec/Testing/QdecUtilitiesTest1.cxx]
 * QdecModuleLibs [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/QdecModule/Testing/QdecModuleLibs.tcl Modules/QdecModule/Testing/QdecModuleLibs.tcl]
 ===Known bugs===

Modules:QDECModule-Documentation-3.6 - Revision history

Nicole at 22:57, 26 March 2010

Nicole: /* Usage */

Nicole: /* Tests */

Nicole: Created page with '__NOTOC__ ===QDEC=== QDEC {| |QDEC GUI and inflated brain |QDEC Plot window |} == Gener…'

Nicole: Created page with 'NOTOC ===QDEC=== QDEC {| |QDEC GUI and inflated brain |QDEC Plot window |} == Gener…'