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