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Integrating QDEC with Slicer3

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Integrating QDEC with Slicer3. Nicole Aucoin. Overview.

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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

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

  • 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
  • Subject populations also can be downloaded from the OASIS brains project stored in an XNAT database at
  • Slicer3 can load .xar archive files direct from a web page download
xnat oasis1
  • Inspect a data set and select it for download
  • Once subjects are downloaded, run FreeSurfer processing pipelines locally and set up a qdec directory with a qdec.table.dat file
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
  • Set up an analysis using the web form, selecting discrete and continuous variables, and morphometric measures
  • Click “Analyze”
xnat qdec4
  • 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
  • Select “Download XAR”, open with Slicer3
xnat qdec6
  • 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 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
  • 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
  • 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
  • The Slicer3 GUI provides a point and click interface to plot data at any point on the average brain
  • 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
  • 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
  • Load a qdec.table.dat that describes the subjects you wish to analyse
glm fit2
  • 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
  • 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
  • Set the Design Name, Click on “Age” as the first continuous factor
  • Click on “Run GLM Fit”
glm fit5
  • 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