Integrating QDEC with Slicer3
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Transcript of Integrating QDEC with Slicer3
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Integrating QDEC with Slicer3Nicole Aucoin
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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.
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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
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qdec.table.dat
Sample file:ID Gender Age CSFOAS1_0001_MR1 F 74 1229.0OAS1_0002_MR1 F 55 773.0OAS1_0003_MR1 F 73 1448.0OAS1_0004_MR1 M 28 1286.0OAS1_0005_MR1 M 18 1304.0OAS1_0006_MR1 F 24 909.0
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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”.
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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
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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
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XNAT - OASIS
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XNAT - OASIS
• Inspect a data set and
select it for download
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XNAT - OASIS
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XNAT
• Once subjects are downloaded, run
FreeSurfer processing pipelines locally
and set up a qdec directory with a
qdec.table.dat file
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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
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XNAT - QDEC
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XNAT - QDEC
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XNAT - QDEC
• Set up an analysis
using the web form,
selecting discrete and
continuous variables,
and morphometric
measures
• Click “Analyze”
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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
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XNAT - QDEC
• Select “Download XAR”, open with Slicer3
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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
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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
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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
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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
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Plotting
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Plotting
• The Slicer3 GUI provides a point and click
interface to plot data at any point on the
average brain
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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
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Plotting
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Inspecting Data
• You can inspect all the statistical results
of the analysis by switching to different
overlays using the “Questions” menu
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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
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GLM Fit
• Load a qdec.table.dat
that describes the
subjects you wish to
analyse
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• Subject ID and other
variable values are
loaded into the table
• Valid discrete and
continuous factors are
set up in the Design
section
GLM Fit
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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
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• Set the Design Name,
Click on “Age” as the first
continuous factor
• Click on “Run GLM Fit”
GLM Fit
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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
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Inspect analysis results
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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