Integrating QDEC with Slicer3
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Integrating QDEC with Slicer3. Nicole Aucoin. Overview.

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Presentation Transcript

Overview

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.

These slides cover where to get data, how to load it,

how to inspect it, and how to run your own analyses.


Sample data
Sample Data

  • 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 population


Qdec table dat
qdec.table.dat

Sample file:

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


Factors
Factors

  • The first column is the subject id, the directory name

  • There are discrete and continuous factors in the following columns for the data table

  • The levels that the discrete factors can take on are specified in a separate file, e.g. for the Gender column, the values can be either “M” or “F”.


Average subject
Average Subject

  • 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


XNAT

  • Subject populations also can be downloaded from the OASIS brains project stored in an XNAT database at http://central.xnat.org/

  • Slicer3 can load .xar archive files direct from a web page download



Xnat oasis1
XNAT - OASIS

  • Inspect a data set and select it for download



XNAT

  • Once subjects are downloaded, run FreeSurfer processing pipelines locally and set up a qdec directory with a qdec.table.dat file


Xnat qdec
XNAT - QDEC

  • XNAT also provides an interface to run QDEC analyses on the server, so large sets of subject scans do not have to be downloaded to your local machine




Xnat qdec3
XNAT - QDEC

  • Set up an analysis using the web form, selecting discrete and continuous variables, and morphometric measures

  • Click “Analyze”


Xnat qdec4
XNAT - QDEC

  • The server will start an analysis on the data you selected using the factors and measures you set up

  • You will get an email when your data is ready for download


Xnat qdec5
XNAT - QDEC

  • Select “Download XAR”, open with Slicer3


Xnat qdec6
XNAT - QDEC

  • Slicer3 will load the downloaded .xar file and extract it to a temporary directory

  • Inside the temporary directory is a .qdec file and Slicer3's data loader interface will give you the option to load it into Slicer3


Slicer3
Slicer3

  • Slicer3 has a QDEC library that will 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


Slicer31
Slicer3

  • The .qdec archive holds a qdec.table.dat file that describes the subjects that were used in the group analysis, and that information is loaded in the QdecModule GUI (to the left in the previous slide)

  • The discrete and continuous factors are also loaded in the GUI


Plotting
Plotting

  • When loading a .qdec file, the first point in the average brain is used to pop up a plot of all the subject values at that vertex, in this example, cortical thickness versus age for the two genders



Plotting2
Plotting

  • The Slicer3 GUI provides a point and click interface to plot data at any point on the average brain


Plotting3
Plotting

  • The next slide shows the toggle to switch to plot mode circled, and a fiducial placed on the brain where the vertex was chosen

  • The plot window shows the RAS and index of the chosen vertex



Inspecting data
Inspecting Data

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


Glm fit
GLM Fit

  • On machines that have a FreeSurfer binary installation, you can use Slicer3 to set up queries and launch the mri_glmfit executable

  • Slicer3 will automatically load the processing results for inspection


Glm fit1
GLM Fit

  • Load a qdec.table.dat that describes the subjects you wish to analyse


Glm fit2
GLM Fit

  • Subject ID and other variable values are loaded into the table

  • Valid discrete and continuous factors are set up in the Design section


Glm fit3
GLM Fit

  • Select the factors that you wish to analyse, e.g. Age, and the measures, e.g. Using the left hemisphere of the brain, thickness, and smoothing of 10

  • If the original pipeline didn't calculate some of these values, Slicer will return an error


Glm fit4
GLM Fit

  • Set the Design Name, Click on “Age” as the first continuous factor

  • Click on “Run GLM Fit”


Glm fit5
GLM Fit

  • Slicer launches mri_glmfit and loads results

  • Average brain is loaded, and a default overlay is set up via the Questions menu

  • A plot window is set up with vertex 0 data shown, and then the user can plot other data points



Query atlas
Query Atlas

  • 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


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