Transcript Introduction

Slicer Tutorial 6
Module: vtkFreeSurferReaders
Sonia Pujol, Ph.D.
Randy Gollub, M.D., Ph.D.
Surgical Planning Laboratory
-1-
http://www.slicer.org
Brigham and Women’s Hospital
Acknowledgments
National Alliance for Medical Image Computing
NIH U54EB005149
Neuroimage Analysis Center
NIH P41RR013218
Center for Functional Neuroimaging Technologies
NIH P41RR14075
Morphometry Biomedical Informatics Research Network
NIH U24 RRO21382
Surgical Planning Laboratory
Thanks to Nicole Aucoin
Surgical Planning Laboratory
-2-
http://www.slicer.org
Brigham and Women’s Hospital
Disclaimer
It is the responsibility of the user of 3DSlicer
and FreeSurfer to comply with both the terms
of the licenses and with the applicable laws,
regulations and rules.
Surgical Planning Laboratory
-3-
http://www.slicer.org
Brigham and Women’s Hospital
Materials Needed
• Slicer 2.5MGH
http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.5MGH_Getting_Started
• Free Surfer Sample Data: FreesurferSubjects.zip
http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101
Surgical Planning Laboratory
-4-
http://www.slicer.org
Brigham and Women’s Hospital
Goal of this tutorial
Guide you step-by-step
through the process of
loading and viewing
FreeSurfer segmentation,
surface reconstruction
and parcellation results
within Slicer.
Surgical Planning Laboratory
-5-
http://www.slicer.org
Brigham and Women’s Hospital
Prerequisites
This tutorial assumes a working
knowledge of how to use
FreeSurfer to generate the
segmentation and surface files.
Tutorial materials for FreeSurfer
are available at
https://surfer.nmr.mgh.harvard.edu/fswiki
https://surfer.nmr.mgh.harvard.edu/docs/ft
p/pub/docs/fsTutorial/
Surgical Planning Laboratory
-6-
http://www.slicer.org
Brigham and Women’s Hospital
Prerequisites
This tutorial assumes a basic
knowledge of how to use
3DSlicer.
Slicer Training 1: Loading
and Viewing Data
Slicer Training 7: Saving Data
http://www.namic.org/Wiki/index.php/
Slicer:Workshops:User_Training_101
Surgical Planning Laboratory
-7-
http://www.slicer.org
Brigham and Women’s Hospital
vtkFreeSurferReaders Module
Surgical Planning Laboratory
-8-
http://www.slicer.org
Brigham and Women’s Hospital
Loading FreeSurfer Data
Slicer can load
• Brain Volumes …………………….
• ASEG Volumes ………………………
• Surfaces…………………………………
• Overlays ………………………………….
Surgical Planning Laboratory
-9-
http://www.slicer.org
Brigham and Women’s Hospital
Overview of Training 6
•Part 1: Loading FreeSurfer Volumes
•Part 2: Overlay Brain and Segmentation
•Part 3: Building 3D Models
•Part 4: Loading Surfaces
•Part 5: Group Statistics
Surgical Planning Laboratory
-10-
http://www.slicer.org
Brigham and Women’s Hospital
vtkFreeSurferReaders Module
Select the Menu Modules in
the Main Panel
Select the category IO and the
module vtkFreeSurferReaders
Surgical Planning Laboratory
-11-
http://www.slicer.org
Brigham and Women’s Hospital
vtkFreeSurferReaders Module
The vtkFreeSurferReaders
module appears in the Main
Panel of Slicer.
The Volumes tab comes up by
default.
Surgical Planning Laboratory
-12-
http://www.slicer.org
Brigham and Women’s Hospital
Loading a Brain file
FreeSurfer Pipeline
Intensity corrected
T1 volume
Skull Stripping and
Noise Filtering
Watershed
algorithm
Brain.mgz
Surgical Planning Laboratory
-13-
http://www.slicer.org
Brigham and Women’s Hospital
Loading a Brain file
Select the Tab Volumes in
the FreeSurfer Module
Click on Browse and select
the subject bert
Click on the mri
folder to access the
brain volume.
Surgical Planning Laboratory
-14-
http://www.slicer.org
Brigham and Women’s Hospital
Loading a Brain file
Select the file brain.mgz
Select the data type GrayScale
Click Apply
Surgical Planning Laboratory
-15-
http://www.slicer.org
Brigham and Women’s Hospital
Loading a Brain file
The volume
Brain.mgz
appears in the
Viewer.
Surgical Planning Laboratory
-16-
http://www.slicer.org
Brigham and Women’s Hospital
Loading a Brain file
Click on the V buttons in
the Axial, Sagittal
and Coronal views.
Surgical Planning Laboratory
-17-
http://www.slicer.org
Brigham and Women’s Hospital
Loading a Brain file
The three anatomical
slices appear in the
3D Viewer.
Surgical Planning Laboratory
-18-
http://www.slicer.org
Brigham and Women’s Hospital
Loading an ASEG file
FreeSurfer Pipeline
Intensity corrected
T1 volume
Subcortical
processing
Segmentation
Aseg.mgz
Surgical Planning Laboratory
-19-
http://www.slicer.org
Brigham and Women’s Hospital
Loading an ASEG file
Select the Tab Volumes in
the FreeSurfer Module.
Click on Browse and select
the subject bert
Click on the mri
folder to access the
aseg volume.
Surgical Planning Laboratory
-20-
http://www.slicer.org
Brigham and Women’s Hospital
Loading an ASEG file
Select the file aseg.mgz
Select the data type Label Map
Click on Apply
Surgical Planning Laboratory
-21-
http://www.slicer.org
Brigham and Women’s Hospital
Loading an ASEG file
The volume
aseg.mgz
appears in the
Viewer.
The labels are
superimposed
on the gray
level brain
images.
Surgical Planning Laboratory
-22-
http://www.slicer.org
Brigham and Women’s Hospital
Determining label numbers in an ASEG file
# ColHeaders Index SegId NVoxels Volume_mm3 SegName Mean StdDev Min Max Range
1 1 0 0.0 Left-Cerebral-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000
2 2 245171 245171.0 Left-Cerebral-White-Matter 121.7886 8.0072 40.0000 186.0000
146.0000
3 3 287069 287069.0 Left-Cerebral-Cortex 91.3494 13.8505 31.0000 220.0000 189.0000
4 4 6876 6876.0 Left-Lateral-Ventricle 48.2126 14.3628 25.0000 106.0000 81.0000
5 5 200 200.0 Left-Inf-Lat-Vent 67.3513 10.8024 35.0000 102.0000 67.0000
6 6 0 0.0 Left-Cerebellum-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000
7 7 10514 10514.0 Left-Cerebellum-White-Matter 120.4405 8.5863 43.0000 134.0000 91.0000
8 8 66561 66561.0 Left-Cerebellum-Cortex 98.8117 14.1726 32.0000 211.0000 179.0000
9 9 0 0.0 Left-Thalamus 0.0000 0.0000 0.0000 0.0000 0.0000
10 10 9887 9887.0 Left-Thalamus-Proper 113.5839 10.3047 45.0000 133.0000 88.0000
11 11 3819 3819.0 Left-Caudate 102.9627 12.1416 62.0000 132.0000 70.0000
12 12 6755 6755.0 Left-Putamen 110.0479 7.4787 76.0000 132.0000 56.0000
13 13 2229 2229.0 Left-Pallidum 122.5797 4.2841 105.0000 134.0000 29.0000
14 14 793 793.0 3rd-Ventricle 54.2582 15.3296 28.0000 93.0000 65.0000
15 15 1819 1819.0 4th-Ventricle 51.8305 15.5400 27.0000 108.0000 81.0000
16 16 26616 26616.0 Brain-Stem 113.1949 12.7048 39.0000 136.0000 97.0000
17 17 4489 4489.0 Left-Hippocampus 96.0929 8.6315 56.0000 122.0000 66.0000
18 18 1869 1869.0 Left-Amygdala 94.8671 8.2028 61.0000 118.0000 57.0000
19 19 0 0.0 Left-Insula 0.0000 0.0000 0.0000 0.0000 0.0000
20 20 0 0.0 Left-Operculum 0.0000 0.0000 0.0000 0.0000 0.0000
21 21 0 0.0 Line-1 0.0000 0.0000 0.0000 0.0000 0.0000
22 22 0 0.0 Line-2 0.0000 0.0000 0.0000 0.0000 0.0000
23 23 0 0.0 Line-3 0.0000 0.0000 0.0000 0.0000 0.0000
24 24 1611 1611.0 CSF 59.9684 15.4368 30.0000 107.0000 77.0000
25 25 0 0.0 Left-Lesion 0.0000 0.0000 0.0000 0.0000 0.0000
26 26 733 733.0 Left-Accumbens-area 97.8124 6.7471 67.0000 121.0000 54.0000
27 27 0 0.0 Left-Substancia-Nigra 0.0000 0.0000 0.0000 0.0000 0.0000
28 28 3957 3957.0 Left-VentralDC 117.4001 10.5813 47.0000 135.0000 88.0000
29 29 0 0.0 Left-undetermined 0.0000 0.0000 0.0000 0.0000 0.0000
30 30 56 56.0 Left-vessel 81.5250 7.9485 62.0000 97.0000 35.0000
Surgical Planning Laboratory
-23-
http://www.slicer.org
The file aseg.stats
gives the list of the
available segmented
structures in the
dataset.
Example of the first
30 structures.
Brigham and Women’s Hospital
Determining label numbers in an ASEG file
# ColHeaders Index SegId NVoxels Volume_mm3 SegName Mean StdDev Min Max Range
1 1 0 0.0 Left-Cerebral-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000
2 2 245171 245171.0 Left-Cerebral-White-Matter 121.7886 8.0072 40.0000 186.0000
146.0000
3 3 287069 287069.0 Left-Cerebral-Cortex 91.3494 13.8505 31.0000 220.0000 189.0000
4 4 6876 6876.0 Left-Lateral-Ventricle 48.2126 14.3628 25.0000 106.0000 81.0000
5 5 200 200.0 Left-Inf-Lat-Vent 67.3513 10.8024 35.0000 102.0000 67.0000
6 6 0 0.0 Left-Cerebellum-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000
7 7 10514 10514.0 Left-Cerebellum-White-Matter 120.4405 8.5863 43.0000 134.0000 91.0000
8 8 66561 66561.0 Left-Cerebellum-Cortex 98.8117 14.1726 32.0000 211.0000 179.0000
9 9 0 0.0 Left-Thalamus 0.0000 0.0000 0.0000 0.0000 0.0000
10 10 9887 9887.0 Left-Thalamus-Proper 113.5839 10.3047 45.0000 133.0000 88.0000
11 11 3819 3819.0 Left-Caudate 102.9627 12.1416 62.0000 132.0000 70.0000
12 12 6755 6755.0 Left-Putamen 110.0479 7.4787 76.0000 132.0000 56.0000
13 13 2229 2229.0 Left-Pallidum 122.5797 4.2841 105.0000 134.0000 29.0000
14 14 793 793.0 3rd-Ventricle 54.2582 15.3296 28.0000 93.0000 65.0000
15 15 1819 1819.0 4th-Ventricle 51.8305 15.5400 27.0000 108.0000 81.0000
16 16 26616 26616.0 Brain-Stem 113.1949 12.7048 39.0000 136.0000 97.0000
17 17 4489 4489.0 Left-Hippocampus 96.0929 8.6315 56.0000 122.0000 66.0000
18 18 1869 1869.0 Left-Amygdala 94.8671 8.2028 61.0000 118.0000 57.0000
19 19 0 0.0 Left-Insula 0.0000 0.0000 0.0000 0.0000 0.0000
20 20 0 0.0 Left-Operculum 0.0000 0.0000 0.0000 0.0000 0.0000
21 21 0 0.0 Line-1 0.0000 0.0000 0.0000 0.0000 0.0000
22 22 0 0.0 Line-2 0.0000 0.0000 0.0000 0.0000 0.0000
23 23 0 0.0 Line-3 0.0000 0.0000 0.0000 0.0000 0.0000
24 24 1611 1611.0 CSF 59.9684 15.4368 30.0000 107.0000 77.0000
25 25 0 0.0 Left-Lesion 0.0000 0.0000 0.0000 0.0000 0.0000
26 26 733 733.0 Left-Accumbens-area 97.8124 6.7471 67.0000 121.0000 54.0000
27 27 0 0.0 Left-Substancia-Nigra 0.0000 0.0000 0.0000 0.0000 0.0000
28 28 3957 3957.0 Left-VentralDC 117.4001 10.5813 47.0000 135.0000 88.0000
29 29 0 0.0 Left-undetermined 0.0000 0.0000 0.0000 0.0000 0.0000
30 30 56 56.0 Left-vessel 81.5250 7.9485 62.0000 97.0000 35.0000
Surgical Planning Laboratory
-24-
http://www.slicer.org
The label #10
represents the
Left-Thalamus
Proper.
The corresponding
segmented volume
is available in the
current dataset.
Brigham and Women’s Hospital
Determining label numbers in an ASEG file
# ColHeaders Index SegId NVoxels Volume_mm3 SegName Mean StdDev Min Max Range
1 1 0 0.0 Left-Cerebral-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000
2 2 245171 245171.0 Left-Cerebral-White-Matter 121.7886 8.0072 40.0000 186.0000
146.0000
3 3 287069 287069.0 Left-Cerebral-Cortex 91.3494 13.8505 31.0000 220.0000 189.0000
4 4 6876 6876.0 Left-Lateral-Ventricle 48.2126 14.3628 25.0000 106.0000 81.0000
5 5 200 200.0 Left-Inf-Lat-Vent 67.3513 10.8024 35.0000 102.0000 67.0000
6 6 0 0.0 Left-Cerebellum-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000
7 7 10514 10514.0 Left-Cerebellum-White-Matter 120.4405 8.5863 43.0000 134.0000 91.0000
8 8 66561 66561.0 Left-Cerebellum-Cortex 98.8117 14.1726 32.0000 211.0000 179.0000
9 9 0 0.0 Left-Thalamus 0.0000 0.0000 0.0000 0.0000 0.0000
10 10 9887 9887.0 Left-Thalamus-Proper 113.5839 10.3047 45.0000 133.0000 88.0000
11 11 3819 3819.0 Left-Caudate 102.9627 12.1416 62.0000 132.0000 70.0000
12 12 6755 6755.0 Left-Putamen 110.0479 7.4787 76.0000 132.0000 56.0000
13 13 2229 2229.0 Left-Pallidum 122.5797 4.2841 105.0000 134.0000 29.0000
14 14 793 793.0 3rd-Ventricle 54.2582 15.3296 28.0000 93.0000 65.0000
15 15 1819 1819.0 4th-Ventricle 51.8305 15.5400 27.0000 108.0000 81.0000
16 16 26616 26616.0 Brain-Stem 113.1949 12.7048 39.0000 136.0000 97.0000
17 17 4489 4489.0 Left-Hippocampus 96.0929 8.6315 56.0000 122.0000 66.0000
18 18 1869 1869.0 Left-Amygdala 94.8671 8.2028 61.0000 118.0000 57.0000
19 19 0 0.0 Left-Insula 0.0000 0.0000 0.0000 0.0000 0.0000
20 20 0 0.0 Left-Operculum 0.0000 0.0000 0.0000 0.0000 0.0000
21 21 0 0.0 Line-1 0.0000 0.0000 0.0000 0.0000 0.0000
22 22 0 0.0 Line-2 0.0000 0.0000 0.0000 0.0000 0.0000
23 23 0 0.0 Line-3 0.0000 0.0000 0.0000 0.0000 0.0000
24 24 1611 1611.0 CSF 59.9684 15.4368 30.0000 107.0000 77.0000
25 25 0 0.0 Left-Lesion 0.0000 0.0000 0.0000 0.0000 0.0000
26 26 733 733.0 Left-Accumbens-area 97.8124 6.7471 67.0000 121.0000 54.0000
27 27 0 0.0 Left-Substancia-Nigra 0.0000 0.0000 0.0000 0.0000 0.0000
28 28 3957 3957.0 Left-VentralDC 117.4001 10.5813 47.0000 135.0000 88.0000
29 29 0 0.0 Left-undetermined 0.0000 0.0000 0.0000 0.0000 0.0000
30 30 56 56.0 Left-vessel 81.5250 7.9485 62.0000 97.0000 35.0000
Surgical Planning Laboratory
-25-
http://www.slicer.org
The label #19
representing the
Left-Insula.
The corresponding
segmented volume
is not available in
the current dataset.
Brigham and Women’s Hospital
Overview of Training 6
•Part 1: Loading FreeSurfer Volumes
•Part 2: Overlay Brain and Segmentation
•Part 3: Building 3D Models
•Part 4: Loading Surfaces
•Part 5: Group Statistics
Surgical Planning Laboratory
-26-
http://www.slicer.org
Brigham and Women’s Hospital
Overlay Brain and Segmentation
Click on the button Bg (Background) and select the
volume aseg in the Axial view.
Surgical Planning Laboratory
-27-
http://www.slicer.org
Brigham and Women’s Hospital
Overlay Brain and Segmentation
Move the mouse over the labels in the Axial view.
Surgical Planning Laboratory
-28-
http://www.slicer.org
Brigham and Women’s Hospital
Overlay Brain and Segmentation
The names of the labels appear in the window.
Surgical Planning Laboratory
-29-
http://www.slicer.org
Brigham and Women’s Hospital
Overlay Brain and Segmentation
Find the labels corresponding to the Left Thalamus
Proper, Left Caudate and Left Putamen in the
three anatomical views.
Surgical Planning Laboratory
-30-
http://www.slicer.org
Brigham and Women’s Hospital
Overlay Brain and Segmentation
Left Thalamus Proper = 10
Surgical Planning Laboratory
-31-
http://www.slicer.org
Brigham and Women’s Hospital
Overlay Brain and Segmentation
Left Putamen = 12
Surgical Planning Laboratory
-32-
http://www.slicer.org
Brigham and Women’s Hospital
Overlay Brain and Segmentation
Left Caudate = 11
Surgical Planning Laboratory
-33-
http://www.slicer.org
Brigham and Women’s Hospital
Overlay Brain and Segmentation
Select View3D in the MainMenu
Surgical Planning Laboratory
-34-
http://www.slicer.org
Brigham and Women’s Hospital
Overlay Brain and Segmentation
Drag right mouse
button down in the 3D
Viewer to zoom in.
Surgical Planning Laboratory
-35-
http://www.slicer.org
Brigham and Women’s Hospital
Overlay Brain and Segmentation
The Viewer displays
a zoom view of the
brain and aseg
slices superimposed.
Drag right mouse
button up in the
Viewer to zoom out.
Surgical Planning Laboratory
-36-
http://www.slicer.org
Brigham and Women’s Hospital
Overview of Training 6
•Part 1: Loading FreeSurfer Volumes
•Part 2: Overlay Brain and Segmentation
•Part 3: Building 3D Models
•Part 4: Loading Surfaces
•Part 5: Group Statistics
Surgical Planning Laboratory
-37-
http://www.slicer.org
Brigham and Women’s Hospital
Building a single Model
Select the module ModelMaker in
the MainMenu
Select the panel Create
Select the Volume aseg and
click on the button Label
Surgical Planning Laboratory
-38-
http://www.slicer.org
Brigham and Women’s Hospital
Building a single Model
Slicer displays the Color
Map corresponding to the
structures that FreeSurfer
can segment.
Surgical Planning Laboratory
-39-
http://www.slicer.org
Brigham and Women’s Hospital
Building a single Model
Move the mouse over the
table and select the label of
the right hippocampus
(label 53).
Surgical Planning Laboratory
-40-
http://www.slicer.org
Brigham and Women’s Hospital
Building a single Model
The label of the right
hippocampus appears in
the Create panel.
Click on Create to build the
3D model.
Surgical Planning Laboratory
-41-
http://www.slicer.org
Brigham and Women’s Hospital
Building a single Model
The 3D model of the right
hippocampus appears
in the Viewer.
Switch to the view 3D,
and drag right mouse
button down in the
Viewer to zoom in.
Surgical Planning Laboratory
-42-
http://www.slicer.org
Brigham and Women’s Hospital
Building a single Model
Slicer displays a
zoom view of the right
hippocampus.
Surgical Planning Laboratory
-43-
http://www.slicer.org
Brigham and Women’s Hospital
Building 3D Models
Select the module ModelMaker in
the MainMenu
Select the panel
Create Multiple
Surgical Planning Laboratory
-44-
http://www.slicer.org
Brigham and Women’s Hospital
Building 3D Models
The Panel Create Multiple
provides the interface to build a set of
continuous models from the values in
the interval
[Starting Label, Ending Label]
Select the Volume aseg
and click on the button
Starting Label
Surgical Planning Laboratory
-45-
http://www.slicer.org
Brigham and Women’s Hospital
Building 3D Models
Click on the label
corresponding to the Left
Thalamus Proper
(Label 10).
Surgical Planning Laboratory
-46-
http://www.slicer.org
Brigham and Women’s Hospital
Building 3D Models
The value and the color of the
selected label appear in the panel.
Click on the button Ending Label
Surgical Planning Laboratory
-47-
http://www.slicer.org
Brigham and Women’s Hospital
Building 3D Models
Click on the label
corresponding to the
Left Pallidum
(Label 13).
Surgical Planning Laboratory
-48-
http://www.slicer.org
Brigham and Women’s Hospital
Building 3D Models
Click on Create all to build the
3D models of the selected labels.
Slicer reconstructs the 3D models
from the labels 10,11,12 and 13.
Surgical Planning Laboratory
-49-
http://www.slicer.org
Brigham and Women’s Hospital
Building 3D Models
The 3D models
of the selected
structures
appear inside
the Viewer.
Surgical Planning Laboratory
-50-
http://www.slicer.org
Brigham and Women’s Hospital
Building 3D Models
Left click
and move
the mouse
to orient the
models in
the Viewer
Surgical Planning Laboratory
-51-
http://www.slicer.org
Brigham and Women’s Hospital
Building 3D Models
Click in the module Models in
the Main Menu and select the
panel Display.
The list of models appears
in the panel.
Deselect the models of the Left
Putamen and Left Caudate.
Surgical Planning Laboratory
-52-
http://www.slicer.org
Brigham and Women’s Hospital
Building 3D Models
Slicer displays the left
Thalamus Proper,
left Pallidum and
right Hippocampus
in the Viewer.
Surgical Planning Laboratory
-53-
http://www.slicer.org
Brigham and Women’s Hospital
Building 3D Models
Click on Show None to make
all the models disappear from
the Scene.
Surgical Planning Laboratory
-54-
http://www.slicer.org
Brigham and Women’s Hospital
Overview of Training 6
•Part 1: Loading FreeSurfer Volumes
•Part 2: Overlay Brain and Segmentation
•Part 3: Building 3D Models
•Part 4: Loading Surfaces
•Part 5: Group Statistics
Surgical Planning Laboratory
-55-
http://www.slicer.org
Brigham and Women’s Hospital
Loading Surfaces
Select the panel Models in the
vtkFreeSurferReaders module.
Click on Browse and
select the surface
lh.white in the directory
subjects/bert/surf
Surgical Planning Laboratory
-56-
http://www.slicer.org
Brigham and Women’s Hospital
Loading Surfaces
The name of the surface selected
appears in the Models panel.
Click Apply to load
the surface in Slicer.
Surgical Planning Laboratory
-57-
http://www.slicer.org
Brigham and Women’s Hospital
Loading Surface
The surface of the
white matter of the left
hemisphere appears
in the Viewer.
Surgical Planning Laboratory
-58-
http://www.slicer.org
Brigham and Women’s Hospital
Parcellation Visualization
In the panel Models
click on aparc to select
the parcellation map of
the model lh.white
Click on Apply to load
the overlay.
Surgical Planning Laboratory
-59-
http://www.slicer.org
Brigham and Women’s Hospital
Parcellation Visualization
Slicer displays the
parcellation results
overlaid on the white
matter surface in the
Viewer.
Switch to 3D view
in the main menu
and zoom in the
model.
Surgical Planning Laboratory
-60-
http://www.slicer.org
Brigham and Women’s Hospital
Parcellation Visualization
Cortical
parcellation of
the white matter
surface in the left
hemisphere.
Surgical Planning Laboratory
-61-
http://www.slicer.org
Brigham and Women’s Hospital
Overview of Training 6
•Part 1: Loading FreeSurfer Volumes
•Part 2: Overlay Brain and Segmentation
•Part 3: Building 3D Models
•Part 4: Loading Surfaces
•Part 5: Group Statistics
Surgical Planning Laboratory
-62-
http://www.slicer.org
Brigham and Women’s Hospital
Group Statistics
•After completion of surface reconstruction for all
subjects in a study, FreeSurfer can perform group
averaging and statistical inference of the cortical
surface measurements such as thickness.
•The observed data is a set of cortical surface
measurements at each vertex for each subject in the
group.
•The process fits a General Linear Model at each
vertex to summarize the data from all the subjects.
•The group analysis results in a statistical
parametric map that can be loaded into Slicer for
visualisation as an overlay on the average surface.
Surgical Planning Laboratory
-63-
http://www.slicer.org
Brigham and Women’s Hospital
Group Statistics
Average Subject
creation
General Linear Modeling
Statistical Parametric Map
Surgical Planning Laboratory
-64-
http://www.slicer.org
Brigham and Women’s Hospital
Group Statistics - example
For my cohort of x sujects, does cortical thickness
vary with age?
Average Subject creation
lh.pial_avg
General Linear Modeling
y_doss_thickness-100lh.fsgd
Statistical Parametric Map
sigt_Age_dossthickness-100lh.w
Surgical Planning Laboratory
-65-
http://www.slicer.org
Brigham and Women’s Hospital
Group Statistics
Select the Tab Models in the
vtkFreeSurferReaders module.
Click on Browse and select the
surface lh.pial_avg in the
directory subjects/average/surf
Surgical Planning Laboratory
-66-
http://www.slicer.org
Brigham and Women’s Hospital
Group Statistics
Select the Tab Display in the
vtkFreeSurferReaders module.
Click on Browse and select the overlay
subjects/stats/sigt_Age_dossthickness-100lh.w
Click on Load Scalar File.
Surgical Planning Laboratory
-67-
http://www.slicer.org
Brigham and Women’s Hospital
Group Statistics
Move the model with
the mouse to update
the Viewer display.
Slicer displays the
statistical map as an
overlay superimposed
on the average surface.
Surgical Planning Laboratory
-68-
http://www.slicer.org
Brigham and Women’s Hospital
Group Statistics
Select the Panel Plot in the
vtkFreeSurferReaders module.
Click on Browse and select the file
y_doss-thickness-100lh.fsgd in
the directory subjects/stats.
Surgical Planning Laboratory
-69-
http://www.slicer.org
Brigham and Women’s Hospital
Group Statistics
Select the Active Model
lh.pial_avg in the list of
models.
Click on Apply to load the
Group Statistics results.
Surgical Planning Laboratory
-70-
http://www.slicer.org
Brigham and Women’s Hospital
Group Statistics
Slicer displays
statistical
distribution of
the cortical
thickness of the
left hemisphere
parameterized by
the age of the
population.
Surgical Planning Laboratory
-71-
http://www.slicer.org
Brigham and Women’s Hospital
Group Statistics
Select the Mode
subject in the
Group Statistics
Window.
Surgical Planning Laboratory
-72-
http://www.slicer.org
Brigham and Women’s Hospital
Group Statistics
Slicer displays the
subjects included
in the Statistical
Analysis.
Move the mouse
over the subjects
table and select
the subject #108.
Surgical Planning Laboratory
-73-
http://www.slicer.org
Brigham and Women’s Hospital
Group Statistics
A red circle shows
the position of the
subject #108 in
the analysis.
Surgical Planning Laboratory
-74-
http://www.slicer.org
Brigham and Women’s Hospital
Group Statistics
The Configure
Classes menu displays
the visualization options of
the population.
Surgical Planning Laboratory
-75-
http://www.slicer.org
Brigham and Women’s Hospital
Group Statistics
Select the pattern
diamond and the
color black for the
male subjects.
Select the pattern
circle and the color
purple for the female
subjects.
Surgical Planning Laboratory
-76-
http://www.slicer.org
Brigham and Women’s Hospital
Group Statistics
Slicer updates the
interface with the
new configuration
parameters.
Surgical Planning Laboratory
-77-
http://www.slicer.org
Brigham and Women’s Hospital
Group Statistics
To generate a plot for a particular vertex, select a
point by clicking on the parametric map at that
vertex on the 3D model in the Viewer
Surgical Planning Laboratory
-78-
http://www.slicer.org
Brigham and Women’s Hospital
Group Statistics
Slicer updates the thickness results with the values
corresponding to the selected vertex.
Surgical Planning Laboratory
-79-
http://www.slicer.org
Brigham and Women’s Hospital
Conclusion
• 3D visualization of brain segmented
surfaces, parcellation maps and
statistical results from FreeSurfer
• Intuitive graphical user interface to
interact with the data
• Open-Source environment
Surgical Planning Laboratory
-80-
http://www.slicer.org
Brigham and Women’s Hospital