Integrating QDEC with Slicer3Nicole Aucoin

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

Plotting

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

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

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

Inspect analysis results

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