integrating qdec with slicer3 click to add subtitle
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Integrating QDEC with Slicer3Click to add subtitle
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
• 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 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
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
• 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 - OASIS
XNAT - OASIS
• Inspect a data set
and select it for
download
XNAT - OASIS
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 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 - QDEC
XNAT - QDEC
XNAT - QDEC
• Set up an analysis
using the web form,
selecting discrete
and continuous
variables, and
morphometric
measures
• Click “Analyze”
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 - QDEC
• Select “Download XAR”, open with Slicer3
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 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
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
• 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
Slicer3
Plotting
• The Slicer3 GUI provides a point and click
interface to plot data at any point on the
average brain
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
Plotting
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 Fit
• Load a
qdec.table.dat
that describes
the subjects you
wish to analyse
• 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
• 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
• Set the Design Name,
Click on “Age” as the
first continuous factor
• Click on “Run GLM Fit”
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
• 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